chr10-44507731-A-G

Variant names:

• chr10-44507731-A-G
• rs915085

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 0.868 in 152,160 control chromosomes in the GnomAD database, including 57,650 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 0.87 (57650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 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: 0.868 AC: 131992 AN: 152044 Hom.: 57611 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.895

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

GnomAD4 genome AF: 0.868 AC: 132090 AN: 152160 Hom.: 57650 Cov.: 32 AF XY: 0.867 AC XY: 64507 AN XY: 74396

African (AFR) AF: 0.779 AC: 32319 AN: 41494

American (AMR) AF: 0.903 AC: 13813 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2866 AN: 3470

East Asian (EAS) AF: 0.767 AC: 3948 AN: 5146

South Asian (SAS) AF: 0.807 AC: 3888 AN: 4820

European-Finnish (FIN) AF: 0.898 AC: 9522 AN: 10600

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62769 AN: 68018

Other (OTH) AF: 0.896 AC: 1894 AN: 2114

Alfa AF: 0.907 Hom.: 114926

Bravo AF: 0.865

Asia WGS AF: 0.788 AC: 2745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.43
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs915085; hg19: chr10-45003179;