rs4291

Positions:

• chr17-63476833-T-A
• chr17-63476833-T-C

Variant summary

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

The variant allele was found at a frequency of 0.634 in 151,724 control chromosomes in the GnomAD database, including 30,526 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.63 (30526 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 17-63476833-T-A is Benign according to our data. Variant chr17-63476833-T-A is described in ClinVar as [Benign]. Clinvar id is 1231511.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96109 AN: 151614 Hom.: 30493 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.558

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.624

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

GnomAD4 genome AF: 0.634 AC: 96188 AN: 151724 Hom.: 30526 Cov.: 31 AF XY: 0.634 AC XY: 47024 AN XY: 74144

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.639

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.619

Alfa AF: 0.621 Hom.: 3451

Bravo AF: 0.637

Asia WGS AF: 0.642 AC: 2220 AN: 3458

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

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.8
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4291; hg19: chr17-61554194;