chr2-84449762-T-TA

Position:

• chr2-84449762-T-TA

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS1

The ENST00000393868.7(SUCLG1):​c.98-11_98-10insT variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0017 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00048 (0 hom.)
• Consequence: SUCLG1 ENST00000393868.7 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

SUCLG1 (HGNC:11449): (succinate-CoA ligase GDP/ADP-forming subunit alpha) This gene encodes the alpha subunit of the heterodimeric enzyme succinate coenzyme A ligase. This enzyme is targeted to the mitochondria and catalyzes the conversion of succinyl CoA and ADP or GDP to succinate and ATP or GTP. Mutations in this gene are the cause of the metabolic disorder fatal infantile lactic acidosis and mitochondrial DNA depletion. [provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00171 (154/90122) while in subpopulation NFE AF= 0.00288 (128/44420). AF 95% confidence interval is 0.00248. There are 0 homozygotes in gnomad4. There are 63 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SUCLG1	NM_003849.4	c.98-11_98-10insT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000393868.7	NP_003840.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7	c.98-11_98-10insT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_003849.4	ENSP00000377446	P1

Frequencies

GnomAD3 genomes AF: 0.00171 AC: 154 AN: 90116 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000720

Gnomad AMI AF: 0.00161

Gnomad AMR AF: 0.000359

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00128

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00288

Gnomad OTH AF: 0.000861

GnomAD4 exome AF: 0.000479 AC: 336 AN: 701696 Hom.: 0 Cov.: 0 AF XY: 0.000452 AC XY: 165 AN XY: 365156

Gnomad4 AFR exome AF: 0.000193

Gnomad4 AMR exome AF: 0.000102

Gnomad4 ASJ exome AF: 0.000123

Gnomad4 EAS exome AF: 0.0000337

Gnomad4 SAS exome AF: 0.000275

Gnomad4 FIN exome AF: 0.000176

Gnomad4 NFE exome AF: 0.000585

Gnomad4 OTH exome AF: 0.000499

GnomAD4 genome AF: 0.00171 AC: 154 AN: 90122 Hom.: 0 Cov.: 0 AF XY: 0.00152 AC XY: 63 AN XY: 41578

Gnomad4 AFR AF: 0.000719

Gnomad4 AMR AF: 0.000359

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00129

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00288

Gnomad4 OTH AF: 0.000852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs56733272; hg19: chr2-84676886;