rs2204502

Variant names:

• chr13-84739259-A-G
• rs2204502

Your query was ambiguous. Multiple possible variants found:

• chr13-84739259-A-G
• chr13-84739259-A-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 0.4 in 151,930 control chromosomes in the GnomAD database, including 13,364 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 0.40 (13364 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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: 0.400 AC: 60718 AN: 151812 Hom.: 13364 Cov.: 31

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.400 AC: 60719 AN: 151930 Hom.: 13364 Cov.: 31 AF XY: 0.393 AC XY: 29202 AN XY: 74234

African (AFR) AF: 0.237 AC: 9804 AN: 41448

American (AMR) AF: 0.353 AC: 5380 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1071 AN: 5170

South Asian (SAS) AF: 0.440 AC: 2119 AN: 4820

European-Finnish (FIN) AF: 0.424 AC: 4470 AN: 10546

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 34954 AN: 67908

Other (OTH) AF: 0.409 AC: 863 AN: 2112

Alfa AF: 0.468 Hom.: 55134

Bravo AF: 0.384

Asia WGS AF: 0.334 AC: 1163 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.29
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2204502; hg19: chr13-85313394;