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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.228 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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0606

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.202

Alfa AF: 0.102 Hom.: 1815

Bravo AF: 0.245

Asia WGS AF: 0.0730 AC: 252 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs492478; hg19: chr5-3939476;