7-131680684-G-A

Variant names:

• chr7-131680684-G-A
• rs7795093

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 0.33 in 152,164 control chromosomes in the GnomAD database, including 8,947 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 0.33 (8947 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.385 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: 0.330 AC: 50177 AN: 152044 Hom.: 8944 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.00846

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.330 AC: 50195 AN: 152164 Hom.: 8947 Cov.: 33 AF XY: 0.326 AC XY: 24267 AN XY: 74404

African (AFR) AF: 0.276 AC: 11479 AN: 41520

American (AMR) AF: 0.276 AC: 4219 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1332 AN: 3466

East Asian (EAS) AF: 0.00867 AC: 45 AN: 5190

South Asian (SAS) AF: 0.247 AC: 1189 AN: 4822

European-Finnish (FIN) AF: 0.387 AC: 4090 AN: 10568

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26416 AN: 67986

Other (OTH) AF: 0.341 AC: 721 AN: 2114

Alfa AF: 0.362 Hom.: 43443

Bravo AF: 0.318

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.20
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs7795093; hg19: chr7-131365443;