5-166529285-G-A

Variant names:

• chr5-166529285-G-A
• rs1450624

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 0.835 in 151,920 control chromosomes in the GnomAD database, including 55,366 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 0.84 (55366 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 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: 0.835 AC: 126803 AN: 151802 Hom.: 55346 Cov.: 30

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.888

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.835 AC: 126870 AN: 151920 Hom.: 55366 Cov.: 30 AF XY: 0.839 AC XY: 62293 AN XY: 74256

African (AFR) AF: 0.556 AC: 22999 AN: 41398

American (AMR) AF: 0.888 AC: 13538 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3184 AN: 3468

East Asian (EAS) AF: 0.771 AC: 3959 AN: 5138

South Asian (SAS) AF: 0.890 AC: 4291 AN: 4822

European-Finnish (FIN) AF: 0.985 AC: 10449 AN: 10610

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.965 AC: 65562 AN: 67926

Other (OTH) AF: 0.860 AC: 1812 AN: 2108

Alfa AF: 0.926 Hom.: 130830

Bravo AF: 0.816

Asia WGS AF: 0.825 AC: 2867 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.97
DANN	Benign	0.67
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs1450624; hg19: chr5-165956290;