rs1176486

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;