5-92731618-G-A

Variant names:

• chr5-92731618-G-A
• rs166085

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 0.645 in 151,816 control chromosomes in the GnomAD database, including 31,825 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 0.64 (31825 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.645 AC: 97831 AN: 151698 Hom.: 31813 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.645 AC: 97881 AN: 151816 Hom.: 31825 Cov.: 31 AF XY: 0.640 AC XY: 47523 AN XY: 74206

African (AFR) AF: 0.637 AC: 26356 AN: 41384

American (AMR) AF: 0.624 AC: 9504 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2275 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1867 AN: 5132

South Asian (SAS) AF: 0.546 AC: 2628 AN: 4814

European-Finnish (FIN) AF: 0.674 AC: 7101 AN: 10530

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46108 AN: 67936

Other (OTH) AF: 0.634 AC: 1339 AN: 2112

Alfa AF: 0.663 Hom.: 5654

Bravo AF: 0.637

Asia WGS AF: 0.484 AC: 1681 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs166085; hg19: chr5-92067325; COSMIC: COSV54960464;