rs13027801

Variant names:

• chr2-142844934-T-C
• rs13027801

Your query was ambiguous. Multiple possible variants found:

• chr2-142844934-T-C
• chr2-142844934-T-G

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 0.382 in 152,040 control chromosomes in the GnomAD database, including 12,046 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 0.38 (12046 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.712
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 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: 0.382 AC: 58076 AN: 151922 Hom.: 12017 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.382 AC: 58149 AN: 152040 Hom.: 12046 Cov.: 32 AF XY: 0.384 AC XY: 28570 AN XY: 74316

African (AFR) AF: 0.541 AC: 22439 AN: 41456

American (AMR) AF: 0.428 AC: 6547 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1005 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5176

South Asian (SAS) AF: 0.464 AC: 2237 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3259 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20045 AN: 67956

Other (OTH) AF: 0.354 AC: 747 AN: 2110

Alfa AF: 0.319 Hom.: 35104

Bravo AF: 0.398

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	4.6
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs13027801; hg19: chr2-143602503;