rs13000344

Variant names:

• chr2-63062599-T-G
• rs13000344

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0275

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.136

Alfa AF: 0.131 Hom.: 694

Bravo AF: 0.117

Asia WGS AF: 0.120 AC: 417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13000344; hg19: chr2-63289734;