chr5-115769132-T-C

Variant names:

• chr5-115769132-T-C
• rs154765

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 0.158 in 152,070 control chromosomes in the GnomAD database, including 2,309 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 0.16 (2309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.426 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: 0.159 AC: 24098 AN: 151952 Hom.: 2306 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.158 AC: 24099 AN: 152070 Hom.: 2309 Cov.: 32 AF XY: 0.158 AC XY: 11734 AN XY: 74332

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.441

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.166

Alfa AF: 0.172 Hom.: 521

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154765; hg19: chr5-115104829;