chr10-44256820-G-A

Variant names:

• chr10-44256820-G-A
• rs2437935

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 0.522 in 151,996 control chromosomes in the GnomAD database, including 22,827 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 0.52 (22827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.643 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: 0.522 AC: 79266 AN: 151878 Hom.: 22828 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.522 AC: 79272 AN: 151996 Hom.: 22827 Cov.: 32 AF XY: 0.521 AC XY: 38679 AN XY: 74282

African (AFR) AF: 0.263 AC: 10910 AN: 41444

American (AMR) AF: 0.554 AC: 8469 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2079 AN: 3460

East Asian (EAS) AF: 0.527 AC: 2717 AN: 5152

South Asian (SAS) AF: 0.480 AC: 2315 AN: 4826

European-Finnish (FIN) AF: 0.640 AC: 6760 AN: 10556

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44080 AN: 67970

Other (OTH) AF: 0.537 AC: 1131 AN: 2106

Alfa AF: 0.593 Hom.: 25416

Bravo AF: 0.504

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.55
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs2437935; hg19: chr10-44752268;