rs2005172

chr17-63918895-A-Cchr17-63918895-A-T

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 0.618 in 1,583,798 control chromosomes in the GnomAD database, including 307,098 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.63 (30870 hom., cov: 32)
  • Exomes 𝑓: 0.62 (276228 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.721

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 17-63918895-A-C is Benign according to our data. Variant chr17-63918895-A-C is described in ClinVar as [Benign]. Clinvar id is 1296532.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95463 AN: 151146 Hom.: 30831 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.617 AC: 883206 AN: 1432536 Hom.: 276228 AF XY: 0.612 AC XY: 435908 AN XY: 712224

Gnomad4 AFR exome AF: 0.711

Gnomad4 AMR exome AF: 0.490

Gnomad4 ASJ exome AF: 0.621

Gnomad4 EAS exome AF: 0.445

Gnomad4 SAS exome AF: 0.426

Gnomad4 FIN exome AF: 0.581

Gnomad4 NFE exome AF: 0.641

Gnomad4 OTH exome AF: 0.606

GnomAD4 genome AF: 0.632 AC: 95552 AN: 151262 Hom.: 30870 Cov.: 32 AF XY: 0.621 AC XY: 45917 AN XY: 73942

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.626

Alfa AF: 0.522 Hom.: 1448

Bravo AF: 0.631

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 12, 2018

This variant is associated with the following publications: (PMID: 18160466, 12655556) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	7.7
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2005172; hg19: chr17-61996255; COSMIC: COSV60110547;