rs2109265

Variant names:

• chr17-62875908-G-A
• rs2109265

Your query was ambiguous. Multiple possible variants found:

• chr17-62875908-G-A
• chr17-62875908-G-C
• chr17-62875908-G-T

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 0.537 in 152,006 control chromosomes in the GnomAD database, including 24,965 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 0.54 (24965 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.536 AC: 81468 AN: 151888 Hom.: 24905 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.537 AC: 81584 AN: 152006 Hom.: 24965 Cov.: 31 AF XY: 0.529 AC XY: 39330 AN XY: 74290

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.490

Alfa AF: 0.434 Hom.: 29449

Bravo AF: 0.544

Asia WGS AF: 0.420 AC: 1462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2109265; hg19: chr17-60953269;