Variant chr17-19337659-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000671102.1(B9D1):c.*61C>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 0.969 in 1,502,002 control chromosomes in the GnomAD database, including 708,316 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.97 ( 71418 hom., cov: 34)

Exomes 𝑓: 0.97 ( 636898 hom. )

Consequence

B9D1
ENST00000671102.1 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.01

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 17-19337659-G-A is Benign according to our data. Variant chr17-19337659-G-A is described in ClinVar as [Benign]. Clinvar id is 1192493.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
B9D1	NM_001321218.2 linkuse as main transcript	c.*61C>T	3_prime_UTR_variant	7/7
B9D1	NM_001321219.2 linkuse as main transcript	c.*26C>T	3_prime_UTR_variant	6/6
B9D1	NM_001368769.2 linkuse as main transcript	c.*61C>T	3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
B9D1	ENST00000582857.2 linkuse as main transcript	c.*61C>T	3_prime_UTR_variant	7/7	4
B9D1	ENST00000671102.1 linkuse as main transcript	c.*61C>T	3_prime_UTR_variant	8/8
B9D1	ENST00000674596.1 linkuse as main transcript	c.*26C>T	3_prime_UTR_variant	8/8
B9D1	ENST00000675510.1 linkuse as main transcript	c.*26C>T	3_prime_UTR_variant	6/6

Frequencies

GnomAD3 genomes

AF:

0.967

AC:

147131

AN:

152214

Hom.:

71371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.991

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.873

Gnomad ASJ

AF:

0.989

Gnomad EAS

AF:

0.852

Gnomad SAS

AF:

0.803

Gnomad FIN

AF:

0.983

Gnomad MID

AF:

0.981

Gnomad NFE

AF:

0.989

Gnomad OTH

AF:

0.969

GnomAD3 exomes

AF:

0.905

AC:

121376

AN:

134102

Hom.:

55664

AF XY:

0.906

AC XY:

66186

AN XY:

73064

show subpopulations

Gnomad AFR exome

AF:

0.991

Gnomad AMR exome

AF:

0.772

Gnomad ASJ exome

AF:

0.987

Gnomad EAS exome

AF:

0.835

Gnomad SAS exome

AF:

0.804

Gnomad FIN exome

AF:

0.986

Gnomad NFE exome

AF:

0.989

Gnomad OTH exome

AF:

0.945

GnomAD4 exome

AF:

0.970

AC:

1308766

AN:

1349670

Hom.:

636898

Cov.:

AF XY:

0.965

AC XY:

641159

AN XY:

664218

show subpopulations

Gnomad4 AFR exome

AF:

0.993

Gnomad4 AMR exome

AF:

0.787

Gnomad4 ASJ exome

AF:

0.986

Gnomad4 EAS exome

AF:

0.863

Gnomad4 SAS exome

AF:

0.810

Gnomad4 FIN exome

AF:

0.985

Gnomad4 NFE exome

AF:

0.990

Gnomad4 OTH exome

AF:

0.963

GnomAD4 genome

AF:

0.967

AC:

147235

AN:

152332

Hom.:

71418

Cov.:

AF XY:

0.960

AC XY:

71539

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.991

Gnomad4 AMR

AF:

0.873

Gnomad4 ASJ

AF:

0.989

Gnomad4 EAS

AF:

0.851

Gnomad4 SAS

AF:

0.805

Gnomad4 FIN

AF:

0.983

Gnomad4 NFE

AF:

0.989

Gnomad4 OTH

AF:

0.969

Alfa

AF:

0.978

Hom.:

64922

Bravo

AF:

0.962

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -

Joubert syndrome 27

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Meckel syndrome, type 9

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.59

DANN

Benign

0.40

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