rs154764

Variant names:

• chr5-115774020-A-G
• rs154764

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 0.17 in 151,878 control chromosomes in the GnomAD database, including 2,475 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 0.17 (2475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 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: 0.170 AC: 25791 AN: 151760 Hom.: 2472 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.153

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.170 AC: 25798 AN: 151878 Hom.: 2475 Cov.: 32 AF XY: 0.169 AC XY: 12557 AN XY: 74204

African (AFR) AF: 0.121 AC: 5021 AN: 41396

American (AMR) AF: 0.170 AC: 2584 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.153 AC: 532 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2249 AN: 5172

South Asian (SAS) AF: 0.170 AC: 816 AN: 4794

European-Finnish (FIN) AF: 0.171 AC: 1799 AN: 10530

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12307 AN: 67966

Other (OTH) AF: 0.176 AC: 370 AN: 2106

Alfa AF: 0.176 Hom.: 337

Bravo AF: 0.171

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.73
DANN	Benign	0.57
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs154764; hg19: chr5-115109717;