7-125751591-A-G

Variant names:

• chr7-125751591-A-G
• rs1419607

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 0.466 in 151,716 control chromosomes in the GnomAD database, including 17,461 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 0.47 (17461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 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: 0.466 AC: 70636 AN: 151598 Hom.: 17460 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.466 AC: 70646 AN: 151716 Hom.: 17461 Cov.: 32 AF XY: 0.464 AC XY: 34411 AN XY: 74126

African (AFR) AF: 0.310 AC: 12854 AN: 41438

American (AMR) AF: 0.408 AC: 6188 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1791 AN: 3460

East Asian (EAS) AF: 0.401 AC: 2053 AN: 5126

South Asian (SAS) AF: 0.412 AC: 1990 AN: 4828

European-Finnish (FIN) AF: 0.609 AC: 6406 AN: 10526

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37693 AN: 67858

Other (OTH) AF: 0.457 AC: 961 AN: 2102

Alfa AF: 0.444 Hom.: 9539

Bravo AF: 0.444

Asia WGS AF: 0.354 AC: 1229 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.75
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1419607; hg19: chr7-125391645;