rs13000470

Variant names:

• chr2-238205577-G-C
• rs13000470

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 0.275 in 151,662 control chromosomes in the GnomAD database, including 6,137 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 0.28 (6137 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 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: 0.276 AC: 41755 AN: 151546 Hom.: 6133 Cov.: 30

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.275 AC: 41768 AN: 151662 Hom.: 6137 Cov.: 30 AF XY: 0.275 AC XY: 20397 AN XY: 74088

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.270

Alfa AF: 0.308 Hom.: 954

Bravo AF: 0.266

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13000470; hg19: chr2-239114218;