chr10-49607466-G-A

Variant names:

• chr10-49607466-G-A
• rs885834

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 0.483 in 152,066 control chromosomes in the GnomAD database, including 20,337 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 0.48 (20337 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 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: 0.483 AC: 73432 AN: 151948 Hom.: 20343 Cov.: 33

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.483 AC: 73416 AN: 152066 Hom.: 20337 Cov.: 33 AF XY: 0.484 AC XY: 35965 AN XY: 74316

African (AFR) AF: 0.229 AC: 9498 AN: 41494

American (AMR) AF: 0.426 AC: 6514 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1890 AN: 3468

East Asian (EAS) AF: 0.240 AC: 1235 AN: 5156

South Asian (SAS) AF: 0.549 AC: 2648 AN: 4822

European-Finnish (FIN) AF: 0.675 AC: 7132 AN: 10572

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42709 AN: 67962

Other (OTH) AF: 0.501 AC: 1057 AN: 2110

Alfa AF: 0.575 Hom.: 44516

Bravo AF: 0.444

Asia WGS AF: 0.405 AC: 1410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.5
DANN	Benign	0.60
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs885834; hg19: chr10-50815512;