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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.850

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.513

Gnomad4 OTH AF: 0.514

Alfa AF: 0.516 Hom.: 12110

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1176486; hg19: chr10-132425539;