rs1881744

Variant names:

• chr12-47421189-G-A
• rs1881744

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 0.0667 in 152,198 control chromosomes in the GnomAD database, including 406 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 0.067 (406 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0885 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: 0.0668 AC: 10156 AN: 152080 Hom.: 408 Cov.: 31

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.0189

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0713

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0904

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0667 AC: 10148 AN: 152198 Hom.: 406 Cov.: 31 AF XY: 0.0642 AC XY: 4780 AN XY: 74422

Gnomad4 AFR AF: 0.0269

Gnomad4 AMR AF: 0.0844

Gnomad4 ASJ AF: 0.0847

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.0713

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.0875

Alfa AF: 0.0665 Hom.: 57

Bravo AF: 0.0668

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.85
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: rs1881744; hg19: chr12-47814972;