rs13000344

Variant names:

• chr2-63062599-T-G
• rs13000344

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 0.116 in 151,940 control chromosomes in the GnomAD database, including 1,355 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 0.12 (1355 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.39
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 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: 0.116 AC: 17571 AN: 151822 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.0275

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.116 AC: 17565 AN: 151940 Hom.: 1355 Cov.: 32 AF XY: 0.121 AC XY: 8973 AN XY: 74268

African (AFR) AF: 0.0275 AC: 1140 AN: 41514

American (AMR) AF: 0.209 AC: 3183 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 650 AN: 3464

East Asian (EAS) AF: 0.186 AC: 962 AN: 5176

South Asian (SAS) AF: 0.152 AC: 731 AN: 4816

European-Finnish (FIN) AF: 0.163 AC: 1722 AN: 10566

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8703 AN: 67830

Other (OTH) AF: 0.136 AC: 286 AN: 2106

Alfa AF: 0.129 Hom.: 1253

Bravo AF: 0.117

Asia WGS AF: 0.120 AC: 417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	6.1
DANN	Benign	0.88
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs13000344; hg19: chr2-63289734;