chr5-115769132-T-C

Variant names:

• chr5-115769132-T-C
• rs154765

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0807 AC: 3348 AN: 41492

American (AMR) AF: 0.174 AC: 2653 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 532 AN: 3464

East Asian (EAS) AF: 0.441 AC: 2275 AN: 5162

South Asian (SAS) AF: 0.172 AC: 831 AN: 4818

European-Finnish (FIN) AF: 0.164 AC: 1736 AN: 10586

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12241 AN: 67962

Other (OTH) AF: 0.166 AC: 350 AN: 2114

Alfa AF: 0.172 Hom.: 829

Bravo AF: 0.159

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.84
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs154765; hg19: chr5-115104829;