5-160542448-T-C

Position:

• chr5-160542448-T-C

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 0.571 in 152,044 control chromosomes in the GnomAD database, including 25,635 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 0.57 (25635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.496

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 (EAS) allele frequency at 95% confidence interval = 0.843 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: 0.571 AC: 86721 AN: 151926 Hom.: 25613 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.634

Gnomad EAS AF: 0.864

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.571 AC: 86787 AN: 152044 Hom.: 25635 Cov.: 32 AF XY: 0.578 AC XY: 42931 AN XY: 74322

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.634

Gnomad4 EAS AF: 0.864

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.584

Alfa AF: 0.594 Hom.: 16575

Bravo AF: 0.572

Asia WGS AF: 0.771 AC: 2683 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	1.3
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4301261; hg19: chr5-159969455;