chr5-160542448-T-C

Variant names:

• chr5-160542448-T-C
• rs4301261

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;