rs1916565

chr10-49677255-G-Achr10-49677255-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;