17-19337913-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000671102.1(B9D1):c.536-165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.967 in 151,084 control chromosomes in the GnomAD database, including 70,880 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.97 (70880 hom., cov: 26)
• Consequence: B9D1 ENST00000671102.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.52

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BP6: Variant 17-19337913-T-C is Benign according to our data. Variant chr17-19337913-T-C is described in ClinVar as [Benign]. Clinvar id is 1292519.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
B9D1	NM_001321218.2	c.473-165A>G		intron_variant
B9D1	NM_001321219.2	c.405-165A>G		intron_variant
B9D1	NM_001368769.2	c.113-165A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
B9D1	ENST00000582857.2	c.113-165A>G		intron_variant		4
B9D1	ENST00000671102.1	c.536-165A>G		intron_variant
B9D1	ENST00000674596.1	c.303-165A>G		intron_variant
B9D1	ENST00000675510.1	c.405-165A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.967 AC: 146052 AN: 150972 Hom.: 70834 Cov.: 26

Gnomad AFR AF: 0.991

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.877

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.968

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.967 AC: 146154 AN: 151084 Hom.: 70880 Cov.: 26 AF XY: 0.961 AC XY: 70879 AN XY: 73722

Gnomad4 AFR AF: 0.990

Gnomad4 AMR AF: 0.877

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.854

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.968

Alfa AF: 0.960 Hom.: 19492

Bravo AF: 0.962

Asia WGS AF: 0.847 AC: 2943 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 26, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.50
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11650112; hg19: chr17-19241226;