chr5-161031029-G-T

Position:

• chr5-161031029-G-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 0.66 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;