chr17-61417213-C-T

Variant names:

• chr17-61417213-C-T
• rs882367

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.611 in 152,166 control chromosomes in the GnomAD database, including 29,073 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 0.61 (29073 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.659 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: 0.612 AC: 92977 AN: 152046 Hom.: 29047 Cov.: 34

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.621

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.611 AC: 93043 AN: 152166 Hom.: 29073 Cov.: 34 AF XY: 0.617 AC XY: 45953 AN XY: 74418

African (AFR) AF: 0.478 AC: 19853 AN: 41522

American (AMR) AF: 0.618 AC: 9449 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3350 AN: 5158

South Asian (SAS) AF: 0.605 AC: 2916 AN: 4822

European-Finnish (FIN) AF: 0.736 AC: 7798 AN: 10598

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45138 AN: 67982

Other (OTH) AF: 0.615 AC: 1299 AN: 2112

Alfa AF: 0.642 Hom.: 50552

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.2
DANN	Benign	0.68
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs882367; hg19: chr17-59494574;