rs12505771

chr4-141445292-G-Achr4-141445292-G-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 0.273 in 151,256 control chromosomes in the GnomAD database, including 7,022 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 0.27 (7022 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.782

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 (AFR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.273 AC: 41265 AN: 151140 Hom.: 6991 Cov.: 31

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0934

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.273 AC: 41361 AN: 151256 Hom.: 7022 Cov.: 31 AF XY: 0.270 AC XY: 19991 AN XY: 73912

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.183

Gnomad4 OTH AF: 0.267

Alfa AF: 0.164 Hom.: 460

Bravo AF: 0.294

Asia WGS AF: 0.226 AC: 787 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	4.3
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12505771; hg19: chr4-142366446;