17-13394477-C-A

Variant names:

• chr17-13394477-C-A
• rs3944086

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.875 in 152,130 control chromosomes in the GnomAD database, including 58,372 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.88 (58372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.843

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133021 AN: 152012 Hom.: 58334 Cov.: 32

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.873

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.875 AC: 133114 AN: 152130 Hom.: 58372 Cov.: 32 AF XY: 0.875 AC XY: 65063 AN XY: 74356

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.910

Gnomad4 ASJ AF: 0.873

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.816

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.883

Alfa AF: 0.887 Hom.: 61793

Bravo AF: 0.877

Asia WGS AF: 0.906 AC: 3150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.67
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3944086; hg19: chr17-13297794; COSMIC: COSV60074381;