rs12612495

Variant names:

• chr2-57714462-C-T
• rs12612495
• ENST00000811253.1:n.149-45041G>A

Variant summary

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

The ENST00000811253.1(ENSG00000285755):​n.149-45041G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,126 control chromosomes in the GnomAD database, including 1,930 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 0.16 (1930 hom., cov: 32)
• Consequence: ENSG00000285755 ENST00000811253.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 2 publications found

Genes affected

ENSG00000285755 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.219 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
ENSG00000285755	ENST00000811253.1	n.149-45041G>A		intron_variant	Intron 2 of 2
ENSG00000285755	ENST00000811255.1	n.396+6487G>A		intron_variant	Intron 1 of 2
ENSG00000305509	ENST00000811399.1	n.393-11233C>T		intron_variant	Intron 2 of 2
ENSG00000305509	ENST00000811400.1	n.134-11233C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23579 AN: 152008 Hom.: 1921 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0790

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.155 AC: 23597 AN: 152126 Hom.: 1930 Cov.: 32 AF XY: 0.158 AC XY: 11757 AN XY: 74360

African (AFR) AF: 0.151 AC: 6267 AN: 41508

American (AMR) AF: 0.106 AC: 1617 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0790 AC: 274 AN: 3468

East Asian (EAS) AF: 0.230 AC: 1192 AN: 5182

South Asian (SAS) AF: 0.180 AC: 866 AN: 4818

European-Finnish (FIN) AF: 0.207 AC: 2194 AN: 10574

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10728 AN: 67986

Other (OTH) AF: 0.154 AC: 324 AN: 2110

Alfa AF: 0.148 Hom.: 2867

Bravo AF: 0.145

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.69
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs12612495; hg19: chr2-57941597;