rs10937544

Variant names:

• chr3-103644217-A-C
• rs10937544

Your query was ambiguous. Multiple possible variants found:

• chr3-103644217-A-C
• chr3-103644217-A-G

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 0.287 in 151,208 control chromosomes in the GnomAD database, including 6,421 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 0.29 (6421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.39
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.394 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: 0.286 AC: 43284 AN: 151090 Hom.: 6397 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.287 AC: 43340 AN: 151208 Hom.: 6421 Cov.: 32 AF XY: 0.297 AC XY: 21948 AN XY: 73840

African (AFR) AF: 0.302 AC: 12520 AN: 41394

American (AMR) AF: 0.359 AC: 5428 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 923 AN: 3456

East Asian (EAS) AF: 0.322 AC: 1637 AN: 5078

South Asian (SAS) AF: 0.409 AC: 1967 AN: 4814

European-Finnish (FIN) AF: 0.376 AC: 3966 AN: 10552

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16075 AN: 67490

Other (OTH) AF: 0.293 AC: 616 AN: 2104

Alfa AF: 0.255 Hom.: 10619

Bravo AF: 0.286

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.038
DANN	Benign	0.40
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10937544; hg19: chr3-103363061;