rs12475512

Positions:

• chr2-231433365-G-A

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 0.469 in 151,870 control chromosomes in the GnomAD database, including 17,505 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 0.47 (17505 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.231433365G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71077 AN: 151752 Hom.: 17470 Cov.: 30

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.469 AC: 71173 AN: 151870 Hom.: 17505 Cov.: 30 AF XY: 0.467 AC XY: 34662 AN XY: 74250

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.471

Alfa AF: 0.455 Hom.: 2010

Bravo AF: 0.474

Asia WGS AF: 0.419 AC: 1459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12475512; hg19: chr2-232298076;