chr12-94548447-T-C

Variant names:

• chr12-94548447-T-C
• rs7139313
• ENST00000307241.5:n.207T>C

Variant summary

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

The ENST00000307241.5(SUCLG2P2):​n.207T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 1,595,280 control chromosomes in the GnomAD database, including 318,870 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 0.67 (34438 hom., cov: 33)
  • Exomes 𝑓: 0.62 (284432 hom.)
• Consequence: SUCLG2P2 ENST00000307241.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.399
• Publications: 8 publications found

Genes affected

SUCLG2P2 (HGNC:43997): (SUCLG2 pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000307241.5. 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
	SUCLG2P2	ENST00000307241.5	TSL:6	n.207T>C		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101412 AN: 151996 Hom.: 34383 Cov.: 33

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.641

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.666

GnomAD4 exome AF: 0.625 AC: 901583 AN: 1443166 Hom.: 284432 Cov.: 29 AF XY: 0.624 AC XY: 448502 AN XY: 719152

African (AFR) AF: 0.752 AC: 24823 AN: 33006

American (AMR) AF: 0.757 AC: 33855 AN: 44698

Ashkenazi Jewish (ASJ) AF: 0.684 AC: 17801 AN: 26034

East Asian (EAS) AF: 0.890 AC: 35231 AN: 39606

South Asian (SAS) AF: 0.623 AC: 53467 AN: 85772

European-Finnish (FIN) AF: 0.617 AC: 32891 AN: 53280

Middle Eastern (MID) AF: 0.613 AC: 2522 AN: 4112

European-Non Finnish (NFE) AF: 0.604 AC: 662645 AN: 1097004

Other (OTH) AF: 0.643 AC: 38348 AN: 59654

GnomAD4 genome AF: 0.667 AC: 101530 AN: 152114 Hom.: 34438 Cov.: 33 AF XY: 0.669 AC XY: 49761 AN XY: 74350

African (AFR) AF: 0.753 AC: 31250 AN: 41512

American (AMR) AF: 0.707 AC: 10810 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3468

East Asian (EAS) AF: 0.874 AC: 4524 AN: 5174

South Asian (SAS) AF: 0.640 AC: 3088 AN: 4822

European-Finnish (FIN) AF: 0.606 AC: 6401 AN: 10560

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41072 AN: 67976

Other (OTH) AF: 0.671 AC: 1413 AN: 2106

Alfa AF: 0.626 Hom.: 126463

Bravo AF: 0.679

Asia WGS AF: 0.783 AC: 2722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	1.3
DANN	Benign	0.32
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs7139313; hg19: chr12-94942223;