rs13408379

Variant names:

• chr2-129715649-G-A
• rs13408379

Your query was ambiguous. Multiple possible variants found:

• chr2-129715649-G-A
• chr2-129715649-G-C
• chr2-129715649-G-T

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 0.21 in 152,104 control chromosomes in the GnomAD database, including 3,828 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 0.21 (3828 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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: 0.210 AC: 31860 AN: 151986 Hom.: 3817 Cov.: 33

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.210 AC: 31911 AN: 152104 Hom.: 3828 Cov.: 33 AF XY: 0.212 AC XY: 15727 AN XY: 74338

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.196

Alfa AF: 0.145 Hom.: 833

Bravo AF: 0.220

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13408379; hg19: chr2-130473222;