5-157076774-C-T

Variant names:

• chr5-157076774-C-T
• rs7725390

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 0.825 in 152,052 control chromosomes in the GnomAD database, including 51,982 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 0.83 (51982 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 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: 0.825 AC: 125342 AN: 151934 Hom.: 51927 Cov.: 30

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.876

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.945

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.825 AC: 125456 AN: 152052 Hom.: 51982 Cov.: 30 AF XY: 0.829 AC XY: 61596 AN XY: 74316

Gnomad4 AFR AF: 0.843

Gnomad4 AMR AF: 0.876

Gnomad4 ASJ AF: 0.901

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.834

Alfa AF: 0.790 Hom.: 8671

Bravo AF: 0.834

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.55
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7725390; hg19: chr5-156503785;