rs4597125

Variant names:

• chr12-76014792-G-A
• rs4597125

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 0.0726 in 152,244 control chromosomes in the GnomAD database, including 820 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 0.073 (820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 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: 0.0726 AC: 11040 AN: 152126 Hom.: 807 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0880

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0542

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0726 AC: 11059 AN: 152244 Hom.: 820 Cov.: 32 AF XY: 0.0835 AC XY: 6216 AN XY: 74428

African (AFR) AF: 0.0175 AC: 728 AN: 41562

American (AMR) AF: 0.0877 AC: 1342 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 249 AN: 3468

East Asian (EAS) AF: 0.357 AC: 1850 AN: 5180

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4822

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10594

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0542 AC: 3685 AN: 67998

Other (OTH) AF: 0.0724 AC: 153 AN: 2114

Alfa AF: 0.0589 Hom.: 613

Bravo AF: 0.0627

Asia WGS AF: 0.311 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.56
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs4597125; hg19: chr12-76408572;