rs13000470

chr2-238205577-G-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;