Variant chr17-19337684-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000671102.1(B9D1):c.*36G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00431 in 1,529,738 control chromosomes in the GnomAD database, including 331 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0065 ( 53 hom., cov: 32)

Exomes 𝑓: 0.0041 ( 278 hom. )

Consequence

B9D1
ENST00000671102.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.442

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 17-19337684-C-A is Benign according to our data. Variant chr17-19337684-C-A is described in ClinVar as [Benign]. Clinvar id is 1175626.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
B9D1	NM_001321218.2 linkuse as main transcript	c.*36G>T	3_prime_UTR_variant	7/7
B9D1	NM_001321219.2 linkuse as main transcript	c.*1G>T	3_prime_UTR_variant	6/6
B9D1	NM_001368769.2 linkuse as main transcript	c.*36G>T	3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
B9D1	ENST00000582857.2 linkuse as main transcript	c.*36G>T	3_prime_UTR_variant	7/7	4
B9D1	ENST00000671102.1 linkuse as main transcript	c.*36G>T	3_prime_UTR_variant	8/8
B9D1	ENST00000674596.1 linkuse as main transcript	c.*1G>T	3_prime_UTR_variant	8/8
B9D1	ENST00000675510.1 linkuse as main transcript	c.*1G>T	3_prime_UTR_variant	6/6

Frequencies

GnomAD3 genomes

AF:

0.00651

AC:

991

AN:

152236

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00166

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0159

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.00661

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000294

Gnomad OTH

AF:

0.00669

GnomAD3 exomes

AF:

0.0125

AC:

1676

AN:

134344

Hom.:

AF XY:

0.0111

AC XY:

814

AN XY:

73184

show subpopulations

Gnomad AFR exome

AF:

0.00140

Gnomad AMR exome

AF:

0.0137

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.115

Gnomad SAS exome

AF:

0.00378

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000228

Gnomad OTH exome

AF:

0.00749

GnomAD4 exome

AF:

0.00406

AC:

5599

AN:

1377384

Hom.:

278

Cov.:

AF XY:

0.00397

AC XY:

2692

AN XY:

678458

show subpopulations

Gnomad4 AFR exome

AF:

0.000825

Gnomad4 AMR exome

AF:

0.0127

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.113

Gnomad4 SAS exome

AF:

0.00440

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000249

Gnomad4 OTH exome

AF:

0.00837

GnomAD4 genome

AF:

0.00649

AC:

989

AN:

152354

Hom.:

Cov.:

AF XY:

0.00731

AC XY:

545

AN XY:

74514

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.0159

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.00621

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000294

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00209

Hom.:

Bravo

AF:

0.00737

Asia WGS

AF:

0.0450

AC:

155

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 31, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.5

DANN

Benign

0.85

Splicing

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