rs7725359

Variant names:

• chr5-83930714-G-A
• rs7725359

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 0.131 in 151,390 control chromosomes in the GnomAD database, including 1,682 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 0.13 (1682 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.192 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: 0.131 AC: 19868 AN: 151272 Hom.: 1683 Cov.: 30

Gnomad AFR AF: 0.0336

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0652

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.131 AC: 19871 AN: 151390 Hom.: 1682 Cov.: 30 AF XY: 0.129 AC XY: 9521 AN XY: 73900

African (AFR) AF: 0.0335 AC: 1383 AN: 41302

American (AMR) AF: 0.103 AC: 1559 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3460

East Asian (EAS) AF: 0.168 AC: 860 AN: 5120

South Asian (SAS) AF: 0.0657 AC: 315 AN: 4798

European-Finnish (FIN) AF: 0.160 AC: 1656 AN: 10372

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13219 AN: 67876

Other (OTH) AF: 0.107 AC: 225 AN: 2098

Alfa AF: 0.173 Hom.: 4789

Bravo AF: 0.122

Asia WGS AF: 0.112 AC: 391 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.46
PhyloP100		-0.057

Splicing

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

Other links and lift over

dbSNP: rs7725359; hg19: chr5-83226533;