chr10-44046117-A-G

Variant names:

• chr10-44046117-A-G
• rs10508881

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 0.505 in 151,988 control chromosomes in the GnomAD database, including 20,015 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 0.50 (20015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.584 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: 0.505 AC: 76648 AN: 151868 Hom.: 20010 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.505 AC: 76682 AN: 151988 Hom.: 20015 Cov.: 32 AF XY: 0.499 AC XY: 37085 AN XY: 74266

African (AFR) AF: 0.388 AC: 16084 AN: 41436

American (AMR) AF: 0.432 AC: 6605 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3466

East Asian (EAS) AF: 0.513 AC: 2645 AN: 5158

South Asian (SAS) AF: 0.459 AC: 2208 AN: 4806

European-Finnish (FIN) AF: 0.529 AC: 5588 AN: 10568

Middle Eastern (MID) AF: 0.459 AC: 134 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 40011 AN: 67958

Other (OTH) AF: 0.500 AC: 1056 AN: 2110

Alfa AF: 0.547 Hom.: 65380

Bravo AF: 0.493

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.9
DANN	Benign	0.65
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs10508881; hg19: chr10-44541565;