rs492478

Variant names:

• chr5-3939362-G-A
• rs492478

Your query was ambiguous. Multiple possible variants found:

• chr5-3939362-G-A
• chr5-3939362-G-T

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 0.228 in 151,698 control chromosomes in the GnomAD database, including 8,059 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 0.23 (8059 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34545 AN: 151580 Hom.: 8018 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.228 AC: 34640 AN: 151698 Hom.: 8059 Cov.: 33 AF XY: 0.224 AC XY: 16595 AN XY: 74126

African (AFR) AF: 0.598 AC: 24776 AN: 41410

American (AMR) AF: 0.110 AC: 1679 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3470

East Asian (EAS) AF: 0.0135 AC: 70 AN: 5178

South Asian (SAS) AF: 0.0606 AC: 292 AN: 4818

European-Finnish (FIN) AF: 0.113 AC: 1186 AN: 10472

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.0845 AC: 5729 AN: 67780

Other (OTH) AF: 0.202 AC: 424 AN: 2102

Alfa AF: 0.121 Hom.: 3522

Bravo AF: 0.245

Asia WGS AF: 0.0730 AC: 252 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.31
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs492478; hg19: chr5-3939476;