10-49677255-G-A

Variant names:

• chr10-49677255-G-A
• rs1916565

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 0.793 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.608 AC: 25177 AN: 41402

American (AMR) AF: 0.793 AC: 12114 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.827 AC: 2868 AN: 3466

East Asian (EAS) AF: 0.807 AC: 4162 AN: 5160

South Asian (SAS) AF: 0.772 AC: 3719 AN: 4816

European-Finnish (FIN) AF: 0.896 AC: 9495 AN: 10596

Middle Eastern (MID) AF: 0.847 AC: 249 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60362 AN: 68002

Other (OTH) AF: 0.813 AC: 1720 AN: 2116

Alfa AF: 0.818 Hom.: 15910

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
PhyloP100		0.046
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1916565; hg19: chr10-50885301;