chr5-115034026-T-G

Variant names:

• chr5-115034026-T-G
• rs13176432

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0318 in 152,296 control chromosomes in the GnomAD database, including 111 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 0.032 (111 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.0318 (4836/152296) while in subpopulation EAS AF = 0.0469 (243/5178). AF 95% confidence interval is 0.0421. There are 111 homozygotes in GnomAd4. There are 2481 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 111 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4830 AN: 152178 Hom.: 112 Cov.: 33

Gnomad AFR AF: 0.00752

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0318 AC: 4836 AN: 152296 Hom.: 111 Cov.: 33 AF XY: 0.0333 AC XY: 2481 AN XY: 74468

African (AFR) AF: 0.00750 AC: 312 AN: 41586

American (AMR) AF: 0.0384 AC: 588 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0363 AC: 126 AN: 3470

East Asian (EAS) AF: 0.0469 AC: 243 AN: 5178

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4828

European-Finnish (FIN) AF: 0.0784 AC: 831 AN: 10598

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0364 AC: 2473 AN: 68018

Other (OTH) AF: 0.0364 AC: 77 AN: 2116

Alfa AF: 0.0331 Hom.: 163

Bravo AF: 0.0287

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.58
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs13176432; hg19: chr5-114369723;