5-161031029-G-T

Variant names:

• chr5-161031029-G-T
• rs938537

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.663 AC: 27474 AN: 41410

American (AMR) AF: 0.547 AC: 8359 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2985 AN: 5146

South Asian (SAS) AF: 0.650 AC: 3126 AN: 4808

European-Finnish (FIN) AF: 0.680 AC: 7175 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46745 AN: 67942

Other (OTH) AF: 0.663 AC: 1402 AN: 2116

Alfa AF: 0.679 Hom.: 17706

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
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs938537; hg19: chr5-160458036;