rs12371985

Positions:

• chr12-94548884-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 90 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG2P2	ENST00000307241.5	n.644G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.0382

Gnomad4 AMR exome AF: 0.0303

Gnomad4 ASJ exome AF: 0.0241

Gnomad4 EAS exome AF: 0.000202

Gnomad4 SAS exome AF: 0.00608

Gnomad4 FIN exome AF: 0.00792

Gnomad4 NFE exome AF: 0.0290

Gnomad4 OTH exome AF: 0.0292

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

Gnomad4 AFR AF: 0.0353

Gnomad4 AMR AF: 0.0464

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00726

Gnomad4 FIN AF: 0.00660

Gnomad4 NFE AF: 0.0307

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0309 Hom.: 18

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12371985; hg19: chr12-94942660;