rs12505771

Variant names:

• chr4-141445292-G-A
• rs12505771

Your query was ambiguous. Multiple possible variants found:

• chr4-141445292-G-A
• chr4-141445292-G-T

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 0.273 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.478 AC: 19720 AN: 41290

American (AMR) AF: 0.299 AC: 4535 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3464

East Asian (EAS) AF: 0.219 AC: 1125 AN: 5148

South Asian (SAS) AF: 0.187 AC: 899 AN: 4796

European-Finnish (FIN) AF: 0.127 AC: 1312 AN: 10352

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.183 AC: 12387 AN: 67730

Other (OTH) AF: 0.267 AC: 563 AN: 2110

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
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs12505771; hg19: chr4-142366446;