7-57429076-A-G

Variant names:

• chr7-57429076-A-G
• rs940331

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 0.348 in 152,004 control chromosomes in the GnomAD database, including 9,555 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 0.35 (9555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.772
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.406 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: 0.348 AC: 52859 AN: 151886 Hom.: 9551 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.348 AC: 52869 AN: 152004 Hom.: 9555 Cov.: 32 AF XY: 0.346 AC XY: 25676 AN XY: 74300

African (AFR) AF: 0.268 AC: 11106 AN: 41446

American (AMR) AF: 0.414 AC: 6321 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1295 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5176

South Asian (SAS) AF: 0.403 AC: 1938 AN: 4812

European-Finnish (FIN) AF: 0.319 AC: 3359 AN: 10546

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26095 AN: 67974

Other (OTH) AF: 0.342 AC: 720 AN: 2108

Alfa AF: 0.375 Hom.: 32205

Bravo AF: 0.355

Asia WGS AF: 0.337 AC: 1170 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	5.1
DANN	Benign	0.70
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs940331; hg19: chr7-57488782;