rs13029479

Variant names:

• chr2-655222-G-A
• rs13029479

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 0.128 in 152,308 control chromosomes in the GnomAD database, including 1,369 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 0.13 (1369 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 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: 0.128 AC: 19469 AN: 152190 Hom.: 1368 Cov.: 34

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.128 AC: 19491 AN: 152308 Hom.: 1369 Cov.: 34 AF XY: 0.126 AC XY: 9393 AN XY: 74470

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.113

Gnomad4 OTH AF: 0.134

Alfa AF: 0.118 Hom.: 732

Bravo AF: 0.133

Asia WGS AF: 0.0810 AC: 279 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	0.20
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13029479; hg19: chr2-655222;