chr5-157022737-G-A

Position:

• chr5-157022737-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 0.213 in 152,094 control chromosomes in the GnomAD database, including 3,691 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 0.21 (3691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 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: 0.213 AC: 32429 AN: 151976 Hom.: 3687 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.213 AC: 32449 AN: 152094 Hom.: 3691 Cov.: 32 AF XY: 0.212 AC XY: 15780 AN XY: 74358

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.216

Alfa AF: 0.195 Hom.: 6224

Bravo AF: 0.216

Asia WGS AF: 0.206 AC: 714 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	0.10
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7707445; hg19: chr5-156449748;