rs12641981

Variant names:

• chr4-45177866-C-T
• rs12641981

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 0.373 in 152,024 control chromosomes in the GnomAD database, including 11,295 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 0.37 (11295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.373 AC: 56685 AN: 151904 Hom.: 11293 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.282

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.373 AC: 56690 AN: 152024 Hom.: 11295 Cov.: 32 AF XY: 0.375 AC XY: 27886 AN XY: 74340

Gnomad4 AFR AF: 0.237

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.397

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.376

Alfa AF: 0.419 Hom.: 19637

Bravo AF: 0.359

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12641981; hg19: chr4-45179883;