rs12641981

Variant names:

• chr4-45177866-C-T
• rs12641981

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.237 AC: 9816 AN: 41464

American (AMR) AF: 0.403 AC: 6147 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1545 AN: 3466

East Asian (EAS) AF: 0.281 AC: 1457 AN: 5176

South Asian (SAS) AF: 0.397 AC: 1911 AN: 4818

European-Finnish (FIN) AF: 0.505 AC: 5344 AN: 10572

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29273 AN: 67948

Other (OTH) AF: 0.376 AC: 793 AN: 2110

Alfa AF: 0.402 Hom.: 29559

Bravo AF: 0.359

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12641981;

hg19: chr4-45179883;