2-84449762-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAA

Position:

• chr2-84449762-TAAAAAAAAAAAAAAA-TAAAAAAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_003849.4(SUCLG1):​c.98-11delT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.021 (34 hom., cov: 0)
  • Exomes 𝑓: 0.0052 (1 hom.)
• Consequence: SUCLG1 NM_003849.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• 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]

SUCLG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 2-84449762-TA-T is Benign according to our data. Variant chr2-84449762-TA-T is described in ClinVar as [Benign]. Clinvar id is 1244208.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.069 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SUCLG1	ENST00000393868.7	c.98-11delT		intron_variant		1	NM_003849.4	ENSP00000377446.2

Frequencies

GnomAD3 genomes AF: 0.0214 AC: 1931 AN: 90030 Hom.: 34 Cov.: 0

Gnomad AFR AF: 0.0719

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0103

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000426

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00943

Gnomad NFE AF: 0.000630

Gnomad OTH AF: 0.0181

GnomAD4 exome AF: 0.00519 AC: 3621 AN: 697062 Hom.: 1 Cov.: 0 AF XY: 0.00503 AC XY: 1826 AN XY: 362678

Gnomad4 AFR exome AF: 0.0187

Gnomad4 AMR exome AF: 0.00302

Gnomad4 ASJ exome AF: 0.00172

Gnomad4 EAS exome AF: 0.000982

Gnomad4 SAS exome AF: 0.00196

Gnomad4 FIN exome AF: 0.00276

Gnomad4 NFE exome AF: 0.00570

Gnomad4 OTH exome AF: 0.00569

GnomAD4 genome AF: 0.0214 AC: 1929 AN: 90034 Hom.: 34 Cov.: 0 AF XY: 0.0214 AC XY: 890 AN XY: 41526

Gnomad4 AFR AF: 0.0718

Gnomad4 AMR AF: 0.0103

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000429

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000630

Gnomad4 OTH AF: 0.0179

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 23, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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;