rs1916565

Variant names:

• chr10-49677255-G-A
• rs1916565

Your query was ambiguous. Multiple possible variants found:

• chr10-49677255-G-A
• chr10-49677255-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 0.793 in 152,032 control chromosomes in the GnomAD database, including 48,989 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 0.79 (48989 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.882 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: 0.794 AC: 120563 AN: 151914 Hom.: 48981 Cov.: 30

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.896

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.793 AC: 120608 AN: 152032 Hom.: 48989 Cov.: 30 AF XY: 0.793 AC XY: 58942 AN XY: 74326

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.793

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.772

Gnomad4 FIN AF: 0.896

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.813

Alfa AF: 0.805 Hom.: 7204

Bravo AF: 0.777

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1916565; hg19: chr10-50885301;