5-2491471-A-T

Variant names:

• chr5-2491471-A-T
• rs462437

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 0.0247 in 97,208 control chromosomes in the GnomAD database, including 285 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 0.025 (285 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.83
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0246 AC: 2388 AN: 97172 Hom.: 284 Cov.: 22

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.00302

Gnomad AMR AF: 0.0105

Gnomad ASJ AF: 0.0188

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0863

Gnomad MID AF: 0.00990

Gnomad NFE AF: 0.0106

Gnomad OTH AF: 0.0154

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

GnomAD4 genome AF: 0.0247 AC: 2397 AN: 97208 Hom.: 285 Cov.: 22 AF XY: 0.0283 AC XY: 1345 AN XY: 47560

African (AFR) AF: 0.0212 AC: 424 AN: 19988

American (AMR) AF: 0.0107 AC: 109 AN: 10218

Ashkenazi Jewish (ASJ) AF: 0.0188 AC: 45 AN: 2394

East Asian (EAS) AF: 0.190 AC: 533 AN: 2798

South Asian (SAS) AF: 0.0242 AC: 80 AN: 3312

European-Finnish (FIN) AF: 0.0863 AC: 663 AN: 7684

Middle Eastern (MID) AF: 0.0156 AC: 3 AN: 192

European-Non Finnish (NFE) AF: 0.0106 AC: 515 AN: 48576

Other (OTH) AF: 0.0166 AC: 23 AN: 1384

Alfa AF: 0.00 Hom.: 5992

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.28
PhyloP100		-5.8

Splicing

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

Other links and lift over

dbSNP: rs462437; hg19: chr5-2491585;