chr17-19337749-C-G

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 4P and 5B. PVS1_StrongBS1_SupportingBS2

The NM_001321218.2(B9D1):c.473-1G>C variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00245 in 1,534,642 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.011 ( 23 hom., cov: 32)

Exomes 𝑓: 0.0015 ( 30 hom. )

Consequence

B9D1
NM_001321218.2 splice_acceptor, intron

Scores

Splicing: ADA: 0.00006013

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1B:4

Conservation

PhyloP100: 0.267

Variant links:

Genes affected

B9D1 (HGNC:24123): (B9 domain containing 1) This gene encodes a B9 domain-containing protein, one of several that are involved in ciliogenesis. Alterations in expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Mar 2016]

B9D1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 6.0958085 fraction of the gene.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0107 (1625/152298) while in subpopulation AFR AF = 0.0355 (1476/41552). AF 95% confidence interval is 0.034. There are 23 homozygotes in GnomAd4. There are 748 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position FAILED quality control check. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAd4 at 23 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
B9D1	NM_001321218.2 link	c.473-1G>C	splice_acceptor_variant, intron_variant	Intron 6 of 6	NP_001308147.1	Q9UPM9
B9D1	NM_001321219.2 link	c.405-1G>C	splice_acceptor_variant, intron_variant	Intron 5 of 5	NP_001308148.1	Q9UPM9A0A6Q8PFJ7
B9D1	NM_001368769.2 link	c.113-1G>C	splice_acceptor_variant, intron_variant	Intron 6 of 6	NP_001355698.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
B9D1	ENST00000671102.1 link	c.536-1G>C	splice_acceptor_variant, intron_variant	Intron 7 of 7		ENSP00000499690.1	A0A590UK40
B9D1	ENST00000675510.1 link	c.405-1G>C	splice_acceptor_variant, intron_variant	Intron 5 of 5		ENSP00000501817.1	A0A6Q8PFJ7
B9D1	ENST00000674596.1 link	c.303-1G>C	splice_acceptor_variant, intron_variant	Intron 7 of 7		ENSP00000501877.1	A0A6Q8PFN7
B9D1	ENST00000582857.2 link	c.113-1G>C	splice_acceptor_variant, intron_variant	Intron 6 of 6	4	ENSP00000463165.2	J3QKN6

Frequencies

GnomAD3 genomes

AF:

0.0106

AC:

1618

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0355

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00478

Gnomad ASJ

AF:

0.00144

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.000617

Gnomad OTH

AF:

0.0105

GnomAD2 exomes

AF:

0.00284

AC:

382

AN:

134390

AF XY:

0.00201

show subpopulations

Gnomad AFR exome

AF:

0.0378

Gnomad AMR exome

AF:

0.00303

Gnomad ASJ exome

AF:

0.00157

Gnomad EAS exome

AF:

0.0000952

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000720

Gnomad OTH exome

AF:

0.00338

GnomAD4 exome

AF:

0.00154

AC:

2135

AN:

1382344

Hom.:

Cov.:

AF XY:

0.00134

AC XY:

914

AN XY:

682074

show subpopulations

Gnomad4 AFR exome

AF:

0.0399

AC:

1260

AN:

31558

Gnomad4 AMR exome

AF:

0.00350

AC:

125

AN:

35688

Gnomad4 ASJ exome

AF:

0.00139

AC:

AN:

25154

Gnomad4 EAS exome

AF:

0.0000280

AC:

AN:

35716

Gnomad4 SAS exome

AF:

0.0000884

AC:

AN:

79204

Gnomad4 FIN exome

AF:

0.00

AC:

AN:

33780

Gnomad4 NFE exome

AF:

0.000410

AC:

442

AN:

1077728

Gnomad4 Remaining exome

AF:

0.00379

AC:

219

AN:

57850

Heterozygous variant carriers

192

287

383

479

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0107

AC:

1625

AN:

152298

Hom.:

Cov.:

AF XY:

0.0100

AC XY:

748

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.0355

AC:

0.0355218

AN:

0.0355218

Gnomad4 AMR

AF:

0.00477

AC:

0.00476999

AN:

0.00476999

Gnomad4 ASJ

AF:

0.00144

AC:

0.00144175

AN:

0.00144175

Gnomad4 EAS

AF:

0.00

AC:

AN:

Gnomad4 SAS

AF:

0.000207

AC:

0.000206868

AN:

0.000206868

Gnomad4 FIN

AF:

0.00

AC:

AN:

Gnomad4 NFE

AF:

0.000617

AC:

0.000617338

AN:

0.000617338

Gnomad4 OTH

AF:

0.0104

AC:

0.010397

AN:

0.010397

Heterozygous variant carriers

154

232

309

386

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00581

Hom.:

Bravo

AF:

0.0123

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000778

AC:

ExAC

AF:

0.00221

AC:

Asia WGS

AF:

0.00289

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1Benign:4

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Benign:2

Jan 31, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Dec 23, 2018

GeneDx

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Joubert syndrome 27

Pathogenic:1

Sep 26, 2019

New York Genome Center

Significance:Likely pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Dec 18, 2023

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The c.473-1G>C variant in B9D1 is classified as benign because it has been identified in 3.5% (1469/41430) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org, v.3.1.2). ACMG/AMP Criteria applied: BA1. -

B9D1-related disorder

Benign:1

Jun 05, 2019

PreventionGenetics, part of Exact Sciences

Significance:Likely benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.85

CADD

Benign

7.8

DANN

Benign

0.52

FATHMM_MKL

Benign

0.096

GERP RS

0.64

Mutation Taster

=100/0

disease causing (ClinVar)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000060

dbscSNV1_RF

Benign

0.0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over