5-159307509-T-C

Variant names:

• chr5-159307509-T-C
• rs11135058

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 0.56 in 152,006 control chromosomes in the GnomAD database, including 24,292 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 0.56 (24292 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

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 = 0.658 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: 0.560 AC: 85047 AN: 151888 Hom.: 24243 Cov.: 31

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.560 AC: 85148 AN: 152006 Hom.: 24292 Cov.: 31 AF XY: 0.562 AC XY: 41750 AN XY: 74306

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.608

Alfa AF: 0.536 Hom.: 5735

Bravo AF: 0.580

Asia WGS AF: 0.658 AC: 2283 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	0.016
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11135058; hg19: chr5-158734517;