rs12371985

Variant names:

• chr12-94548884-G-A
• rs12371985
• ENST00000307241.5:n.644G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000307241.5(SUCLG2P2):​n.644G>A 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 0.0267 in 1,612,742 control chromosomes in the GnomAD database, including 721 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 0.030 (90 hom., cov: 33)
  • Exomes 𝑓: 0.026 (631 hom.)
• Consequence: SUCLG2P2 ENST00000307241.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.905
• Publications: 1 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=-0.75).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0301 (4585/152248) while in subpopulation AMR AF = 0.0464 (709/15290). AF 95% confidence interval is 0.0435. There are 90 homozygotes in GnomAd4. There are 2200 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 90 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUCLG2P2		n.94548884G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUCLG2P2	ENST00000307241.5	n.644G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4583 AN: 152130 Hom.: 90 Cov.: 33

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00704

Gnomad FIN AF: 0.00660

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0307

Gnomad OTH AF: 0.0459

GnomAD4 exome AF: 0.0263 AC: 38482 AN: 1460494 Hom.: 631 Cov.: 35 AF XY: 0.0259 AC XY: 18823 AN XY: 726562

African (AFR) AF: 0.0382 AC: 1279 AN: 33444

American (AMR) AF: 0.0303 AC: 1356 AN: 44722

Ashkenazi Jewish (ASJ) AF: 0.0241 AC: 630 AN: 26136

East Asian (EAS) AF: 0.000202 AC: 8 AN: 39700

South Asian (SAS) AF: 0.00608 AC: 524 AN: 86196

European-Finnish (FIN) AF: 0.00792 AC: 423 AN: 53420

Middle Eastern (MID) AF: 0.0506 AC: 234 AN: 4626

European-Non Finnish (NFE) AF: 0.0290 AC: 32266 AN: 1111992

Other (OTH) AF: 0.0292 AC: 1762 AN: 60258

GnomAD4 genome AF: 0.0301 AC: 4585 AN: 152248 Hom.: 90 Cov.: 33 AF XY: 0.0296 AC XY: 2200 AN XY: 74432

African (AFR) AF: 0.0353 AC: 1467 AN: 41540

American (AMR) AF: 0.0464 AC: 709 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00726 AC: 35 AN: 4824

European-Finnish (FIN) AF: 0.00660 AC: 70 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0307 AC: 2089 AN: 68020

Other (OTH) AF: 0.0454 AC: 96 AN: 2114

Alfa AF: 0.0311 Hom.: 20

Bravo AF: 0.0322

Asia WGS AF: 0.00635 AC: 22 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	2.7
DANN	Benign	0.78
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs12371985; hg19: chr12-94942660;