rs1425132

chr7-37522765-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;