rs12813083

Variant names:

• chr12-62974950-C-T
• rs12813083
• ENST00000826462.1:n.119+7511C>T

Variant summary

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

The ENST00000826462.1(ENSG00000307468):​n.119+7511C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,178 control chromosomes in the GnomAD database, including 478 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 0.076 (478 hom., cov: 32)
• Consequence: ENSG00000307468 ENST00000826462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

Genes affected

ENSG00000307468 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0847 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
ENSG00000307468	ENST00000826462.1	n.119+7511C>T		intron_variant	Intron 1 of 2
ENSG00000307468	ENST00000826463.1	n.183+4515C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0755 AC: 11477 AN: 152060 Hom.: 476 Cov.: 32

Gnomad AFR AF: 0.0756

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0641

Gnomad ASJ AF: 0.0761

Gnomad EAS AF: 0.00365

Gnomad SAS AF: 0.0562

Gnomad FIN AF: 0.0681

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0755 AC: 11492 AN: 152178 Hom.: 478 Cov.: 32 AF XY: 0.0750 AC XY: 5579 AN XY: 74408

African (AFR) AF: 0.0758 AC: 3145 AN: 41498

American (AMR) AF: 0.0640 AC: 978 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0761 AC: 264 AN: 3470

East Asian (EAS) AF: 0.00385 AC: 20 AN: 5190

South Asian (SAS) AF: 0.0572 AC: 276 AN: 4822

European-Finnish (FIN) AF: 0.0681 AC: 721 AN: 10586

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0866 AC: 5887 AN: 68010

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

Alfa AF: 0.0856 Hom.: 509

Bravo AF: 0.0752

Asia WGS AF: 0.0350 AC: 122 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.33
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12813083; hg19: chr12-63368730;