chr5-159133146-C-T

Position:

• chr5-159133146-C-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 0.18 in 152,190 control chromosomes in the GnomAD database, including 2,507 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 0.18 (2507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.180 AC: 27302 AN: 152072 Hom.: 2500 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.180 AC: 27327 AN: 152190 Hom.: 2507 Cov.: 32 AF XY: 0.177 AC XY: 13177 AN XY: 74408

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.180

Alfa AF: 0.181 Hom.: 3482

Bravo AF: 0.174

Asia WGS AF: 0.166 AC: 575 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.75
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs270661; hg19: chr5-158560154; COSMIC: COSV60222392;