rs2005171

chr17-63919116-C-Achr17-63919116-C-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 0.344 in 152,134 control chromosomes in the GnomAD database, including 9,849 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (9849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 17-63919116-C-A is Benign according to our data. Variant chr17-63919116-C-A is described in ClinVar as [Benign]. Clinvar id is 1296534.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.418 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: 0.344 AC: 52269 AN: 152018 Hom.: 9841 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.344 AC: 52300 AN: 152134 Hom.: 9849 Cov.: 33 AF XY: 0.341 AC XY: 25364 AN XY: 74368

Gnomad4 AFR AF: 0.186

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.422

Gnomad4 OTH AF: 0.369

Alfa AF: 0.242 Hom.: 609

Bravo AF: 0.338

Asia WGS AF: 0.332 AC: 1157 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

Nov 12, 2018

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

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2005171; hg19: chr17-61996476;