chr10-31530432-T-G

Variant names:

• chr10-31530432-T-G
• rs11008516

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 0.165 in 149,814 control chromosomes in the GnomAD database, including 2,082 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 0.16 (2082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.165 AC: 24643 AN: 149700 Hom.: 2081 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0538

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.165 AC: 24669 AN: 149814 Hom.: 2082 Cov.: 32 AF XY: 0.160 AC XY: 11732 AN XY: 73238

African (AFR) AF: 0.224 AC: 8809 AN: 39412

American (AMR) AF: 0.125 AC: 1887 AN: 15144

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.0540 AC: 279 AN: 5170

South Asian (SAS) AF: 0.0901 AC: 433 AN: 4808

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10572

Middle Eastern (MID) AF: 0.184 AC: 53 AN: 288

European-Non Finnish (NFE) AF: 0.162 AC: 10979 AN: 67942

Other (OTH) AF: 0.160 AC: 334 AN: 2094

Alfa AF: 0.163 Hom.: 902

Bravo AF: 0.165

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.37
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11008516; hg19: chr10-31819360;