rs10880160

Variant names:

• chr12-41780629-C-T
• rs10880160

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 0.346 in 151,948 control chromosomes in the GnomAD database, including 9,942 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 0.35 (9942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.346 AC: 52506 AN: 151832 Hom.: 9916 Cov.: 32

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.172

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.346 AC: 52579 AN: 151948 Hom.: 9942 Cov.: 32 AF XY: 0.345 AC XY: 25661 AN XY: 74288

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.270

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.294

Gnomad4 OTH AF: 0.310

Alfa AF: 0.292 Hom.: 13457

Bravo AF: 0.343

Asia WGS AF: 0.266 AC: 924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10880160; hg19: chr12-42174431;