12-63015847-T-C

Variant names:

• chr12-63015847-T-C
• rs12823849
• ENST00000826462.1:n.120-6215T>C

Variant summary

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

The ENST00000826462.1(ENSG00000307468):​n.120-6215T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0735 in 152,158 control chromosomes in the GnomAD database, including 464 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 0.074 (464 hom., cov: 32)
• Consequence: ENSG00000307468 ENST00000826462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307468	ENST00000826462.1		n.120-6215T>C		intron	N/A
	ENSG00000307468	ENST00000826463.1		n.184-6215T>C		intron	N/A
	ENSG00000307468	ENST00000826464.1		n.132-6215T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0735 AC: 11179 AN: 152040 Hom.: 464 Cov.: 32

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0553

Gnomad FIN AF: 0.0767

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0721

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

GnomAD4 genome AF: 0.0735 AC: 11190 AN: 152158 Hom.: 464 Cov.: 32 AF XY: 0.0735 AC XY: 5471 AN XY: 74406

African (AFR) AF: 0.0645 AC: 2675 AN: 41502

American (AMR) AF: 0.0650 AC: 992 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0816 AC: 283 AN: 3468

East Asian (EAS) AF: 0.00386 AC: 20 AN: 5180

South Asian (SAS) AF: 0.0564 AC: 272 AN: 4822

European-Finnish (FIN) AF: 0.0767 AC: 813 AN: 10596

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0872 AC: 5929 AN: 67998

Other (OTH) AF: 0.0704 AC: 149 AN: 2116

Alfa AF: 0.0842 Hom.: 683

Bravo AF: 0.0724

Asia WGS AF: 0.0350 AC: 122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs12823849; hg19: chr12-63409627;