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

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;