10-49597937-A-G

Variant names:

• chr10-49597937-A-G
• rs1917805

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 0.417 in 152,116 control chromosomes in the GnomAD database, including 16,536 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 0.42 (16536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.591 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: 0.417 AC: 63440 AN: 151998 Hom.: 16546 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.417 AC: 63405 AN: 152116 Hom.: 16536 Cov.: 32 AF XY: 0.409 AC XY: 30406 AN XY: 74358

African (AFR) AF: 0.113 AC: 4680 AN: 41540

American (AMR) AF: 0.394 AC: 6026 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1684 AN: 3470

East Asian (EAS) AF: 0.345 AC: 1785 AN: 5170

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4808

European-Finnish (FIN) AF: 0.505 AC: 5341 AN: 10584

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

European-Non Finnish (NFE) AF: 0.595 AC: 40457 AN: 67950

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.493 Hom.: 32849

Bravo AF: 0.395

Asia WGS AF: 0.327 AC: 1141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.60
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1917805; hg19: chr10-50805983;