rs12475512

Variant names:

• chr2-231433365-G-A
• rs12475512
• ENST00000757726.1:n.110-723G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000757726.1(ENSG00000233538):​n.110-723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000233538 ENST00000757726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 3 publications found

Genes affected

ENSG00000233538 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000233538	ENST00000757726.1	n.110-723G>A		intron_variant	Intron 1 of 2
ENSG00000233538	ENST00000757727.1	n.109-650G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.601 AC: 24897 AN: 41418

American (AMR) AF: 0.450 AC: 6863 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1836 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1515 AN: 5160

South Asian (SAS) AF: 0.414 AC: 1994 AN: 4818

European-Finnish (FIN) AF: 0.455 AC: 4785 AN: 10520

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27741 AN: 67926

Other (OTH) AF: 0.471 AC: 995 AN: 2112

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
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs12475512; hg19: chr2-232298076;