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. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.319 AC: 13240 AN: 41470

American (AMR) AF: 0.210 AC: 3204 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 454 AN: 3472

East Asian (EAS) AF: 0.264 AC: 1364 AN: 5174

South Asian (SAS) AF: 0.300 AC: 1442 AN: 4812

European-Finnish (FIN) AF: 0.138 AC: 1457 AN: 10564

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10163 AN: 68004

Other (OTH) AF: 0.196 AC: 414 AN: 2112

Alfa AF: 0.148 Hom.: 953

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs13408379; hg19: chr2-130473222;