rs1176486

Variant names:

• chr10-130627275-A-G
• rs1176486

Your query was ambiguous. Multiple possible variants found:

• chr10-130627275-A-G
• chr10-130627275-A-T

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 0.521 in 152,132 control chromosomes in the GnomAD database, including 21,157 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 0.52 (21157 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 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: 0.521 AC: 79203 AN: 152014 Hom.: 21135 Cov.: 34

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.521 AC: 79259 AN: 152132 Hom.: 21157 Cov.: 34 AF XY: 0.531 AC XY: 39524 AN XY: 74368

African (AFR) AF: 0.438 AC: 18169 AN: 41496

American (AMR) AF: 0.603 AC: 9225 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1864 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4396 AN: 5174

South Asian (SAS) AF: 0.621 AC: 2994 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6270 AN: 10572

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34848 AN: 67986

Other (OTH) AF: 0.514 AC: 1087 AN: 2116

Alfa AF: 0.515 Hom.: 15959

Bravo AF: 0.515

Asia WGS AF: 0.711 AC: 2473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.064
DANN	Benign	0.71
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1176486; hg19: chr10-132425539;