rs13006295

Variant names:

• chr2-238205936-G-A
• rs13006295

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 0.277 in 152,180 control chromosomes in the GnomAD database, including 6,245 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 0.28 (6245 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42136 AN: 152062 Hom.: 6240 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.277 AC: 42151 AN: 152180 Hom.: 6245 Cov.: 33 AF XY: 0.277 AC XY: 20618 AN XY: 74406

African (AFR) AF: 0.178 AC: 7378 AN: 41508

American (AMR) AF: 0.254 AC: 3888 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.210 AC: 1092 AN: 5188

South Asian (SAS) AF: 0.368 AC: 1775 AN: 4824

European-Finnish (FIN) AF: 0.334 AC: 3538 AN: 10582

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.334 AC: 22729 AN: 67994

Other (OTH) AF: 0.271 AC: 571 AN: 2110

Alfa AF: 0.310 Hom.: 960

Bravo AF: 0.267

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.31
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs13006295; hg19: chr2-239114577;