rs1425132

Variant names:

• chr7-37522765-A-G
• rs1425132

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 0.428 in 152,068 control chromosomes in the GnomAD database, including 14,174 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 0.43 (14174 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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: 0.428 AC: 64973 AN: 151950 Hom.: 14167 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.428 AC: 65011 AN: 152068 Hom.: 14174 Cov.: 32 AF XY: 0.425 AC XY: 31621 AN XY: 74330

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.452

Alfa AF: 0.472 Hom.: 29868

Bravo AF: 0.427

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425132; hg19: chr7-37562368;