rs481125

Variant names:

• chr10-29170754-T-C
• rs481125

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.00576 in 115,720 control chromosomes in the GnomAD database, including 7 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 0.0058 (7 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00576 (667/115720) while in subpopulation AFR AF = 0.0237 (646/27224). AF 95% confidence interval is 0.0222. There are 7 homozygotes in GnomAd4. There are 304 alleles in the male GnomAd4 subpopulation. Median coverage is 27. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 7 gene

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: 0.00577 AC: 668 AN: 115722 Hom.: 7 Cov.: 27

Gnomad AFR AF: 0.0238

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00133

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000358

Gnomad OTH AF: 0.00190

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

GnomAD4 genome AF: 0.00576 AC: 667 AN: 115720 Hom.: 7 Cov.: 27 AF XY: 0.00542 AC XY: 304 AN XY: 56076

African (AFR) AF: 0.0237 AC: 646 AN: 27224

American (AMR) AF: 0.00132 AC: 16 AN: 12080

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2742

East Asian (EAS) AF: 0.00 AC: 0 AN: 4512

South Asian (SAS) AF: 0.00 AC: 0 AN: 3488

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7190

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 248

European-Non Finnish (NFE) AF: 0.0000358 AC: 2 AN: 55802

Other (OTH) AF: 0.00190 AC: 3 AN: 1578

Alfa AF: 0.00948 Hom.: 0

Bravo AF: 0.00551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.9
DANN	Benign	0.88
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs481125; hg19: chr10-29459683;