rs2781551

Variant names:

• chr10-44366645-C-G
• rs2781551

Your query was ambiguous. Multiple possible variants found:

• chr10-44366645-C-G
• chr10-44366645-C-T

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 0.789 in 152,018 control chromosomes in the GnomAD database, including 47,865 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 (47865 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.864 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: 0.789 AC: 119895 AN: 151900 Hom.: 47833 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.827

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.828

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

GnomAD4 genome AF: 0.789 AC: 119980 AN: 152018 Hom.: 47865 Cov.: 31 AF XY: 0.795 AC XY: 59095 AN XY: 74318

African (AFR) AF: 0.655 AC: 27108 AN: 41416

American (AMR) AF: 0.876 AC: 13394 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2898 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4036 AN: 5138

South Asian (SAS) AF: 0.792 AC: 3806 AN: 4806

European-Finnish (FIN) AF: 0.914 AC: 9695 AN: 10608

Middle Eastern (MID) AF: 0.831 AC: 241 AN: 290

European-Non Finnish (NFE) AF: 0.829 AC: 56337 AN: 67982

Other (OTH) AF: 0.831 AC: 1757 AN: 2114

Alfa AF: 0.810 Hom.: 6241

Bravo AF: 0.782

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.63
DANN	Benign	0.45
PhyloP100		-2.1
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: rs2781551; hg19: chr10-44862093;