rs7725359

Positions:

• chr5-83930714-G-A

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 0.131 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

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 = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.0335

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.107

Alfa AF: 0.175 Hom.: 3581

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725359; hg19: chr5-83226533;