5-175227792-A-G

Variant names:

• chr5-175227792-A-G
• rs998876

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 0.477 in 152,134 control chromosomes in the GnomAD database, including 20,208 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 0.48 (20208 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

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: 0.477 AC: 72439 AN: 152016 Hom.: 20160 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.477 AC: 72535 AN: 152134 Hom.: 20208 Cov.: 32 AF XY: 0.469 AC XY: 34860 AN XY: 74360

African (AFR) AF: 0.776 AC: 32189 AN: 41480

American (AMR) AF: 0.264 AC: 4028 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1557 AN: 5184

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4816

European-Finnish (FIN) AF: 0.397 AC: 4201 AN: 10588

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26627 AN: 67996

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.434 Hom.: 1878

Bravo AF: 0.480

Asia WGS AF: 0.322 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.0
DANN	Benign	0.90
PhyloP100		0.023

Splicing

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

Other links and lift over

dbSNP: rs998876; hg19: chr5-174654795;