rs739719

Positions:

• chr5-132537173-A-C
• chr5-132537173-A-T

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 0.785 in 152,158 control chromosomes in the GnomAD database, including 50,608 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 0.78 (50608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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: 0.785 AC: 119362 AN: 152040 Hom.: 50597 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.884

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.770

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.785 AC: 119393 AN: 152158 Hom.: 50608 Cov.: 32 AF XY: 0.789 AC XY: 58677 AN XY: 74390

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.884

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.823

Alfa AF: 0.908 Hom.: 128488

Bravo AF: 0.762

Asia WGS AF: 0.814 AC: 2832 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs739719; hg19: chr5-131872865;