rs7725292

chr5-148008825-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 0.163 in 152,158 control chromosomes in the GnomAD database, including 2,196 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 0.16 (2196 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24729 AN: 152040 Hom.: 2191 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0789

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.163 AC: 24764 AN: 152158 Hom.: 2196 Cov.: 32 AF XY: 0.160 AC XY: 11899 AN XY: 74392

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.0789

Gnomad4 EAS AF: 0.324

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.170

Alfa AF: 0.152 Hom.: 997

Bravo AF: 0.172

Asia WGS AF: 0.282 AC: 980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.57
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725292; hg19: chr5-147388388;