chr17-19338043-A-G

Position:

• chr17-19338043-A-G

Variant summary

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

The ENST00000671102.1(B9D1):​c.536-295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.966 in 152,314 control chromosomes in the GnomAD database, including 71,388 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.97 (71388 hom., cov: 33)
• Consequence: B9D1 ENST00000671102.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.30

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=-0.92).
• BP6: Variant 17-19338043-A-G is Benign according to our data. Variant chr17-19338043-A-G is described in ClinVar as [Benign]. Clinvar id is 1239791.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
B9D1	NM_001321218.2	c.473-295T>C		intron_variant			NP_001308147.1
B9D1	NM_001321219.2	c.405-295T>C		intron_variant			NP_001308148.1
B9D1	NM_001368769.2	c.113-295T>C		intron_variant			NP_001355698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
B9D1	ENST00000582857.2	c.113-295T>C		intron_variant		4		ENSP00000463165
B9D1	ENST00000671102.1	c.536-295T>C		intron_variant				ENSP00000499690
B9D1	ENST00000674596.1	c.303-295T>C		intron_variant				ENSP00000501877
B9D1	ENST00000675510.1	c.405-295T>C		intron_variant				ENSP00000501817

Frequencies

GnomAD3 genomes AF: 0.966 AC: 147093 AN: 152196 Hom.: 71341 Cov.: 33

Gnomad AFR AF: 0.991

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.983

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: 0.968

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

GnomAD4 genome AF: 0.966 AC: 147197 AN: 152314 Hom.: 71388 Cov.: 33 AF XY: 0.960 AC XY: 71525 AN XY: 74482

Gnomad4 AFR AF: 0.991

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.805

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.968

Alfa AF: 0.971 Hom.: 3351

Bravo AF: 0.962

Asia WGS AF: 0.847 AC: 2947 AN: 3478

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 19, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8079844; hg19: chr17-19241356;