rs10880160

Positions:

• chr12-41780629-C-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 0.346 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;