5-161031029-G-T

Variant names:

• chr5-161031029-G-T
• rs938537

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 0.66 in 151,920 control chromosomes in the GnomAD database, including 33,280 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 0.66 (33280 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 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: 0.660 AC: 100239 AN: 151802 Hom.: 33263 Cov.: 31

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.660 AC: 100309 AN: 151920 Hom.: 33280 Cov.: 31 AF XY: 0.658 AC XY: 48863 AN XY: 74218

Gnomad4 AFR AF: 0.663

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.680

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.663

Alfa AF: 0.678 Hom.: 15707

Bravo AF: 0.650

Asia WGS AF: 0.565 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs938537; hg19: chr5-160458036;