11-791209-G-GCA

Variant summary

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

The NM_001191061.2(SLC25A22):c.*705_*706insTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0614 in 154,546 control chromosomes in the GnomAD database, including 804 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (803 hom., cov: 33)
  • Exomes 𝑓: 0.010 (1 hom.)
• Consequence: SLC25A22 NM_001191061.2 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.659

Genes affected

SLC25A22 (HGNC:19954): (solute carrier family 25 member 22) This gene encodes a mitochondrial glutamate carrier. Mutations in this gene are associated with early infantile epileptic encephalopathy. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-791209-G-GCA is Benign according to our data. Variant chr11-791209-G-GCA is described in ClinVar as [Likely_benign]. Clinvar id is 306248.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC25A22	NM_001191061.2	c.*705_*706insTG		3_prime_UTR_variant	10/10	ENST00000628067.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC25A22	ENST00000628067.3	c.*705_*706insTG		3_prime_UTR_variant	10/10	1	NM_001191061.2	P1
SLC25A22	ENST00000320230.9	c.*705_*706insTG		3_prime_UTR_variant	10/10	1		P1

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9449 AN: 152132 Hom.: 799 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0305

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0555

GnomAD4 exome AF: 0.0100 AC: 23 AN: 2296 Hom.: 1 Cov.: 0 AF XY: 0.00997 AC XY: 13 AN XY: 1304

Gnomad4 AFR exome AF: 0.115

Gnomad4 AMR exome AF: 0.0105

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0294

Gnomad4 NFE exome AF: 0.00949

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0621 AC: 9460 AN: 152250 Hom.: 803 Cov.: 33 AF XY: 0.0592 AC XY: 4410 AN XY: 74458

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.0305

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0549

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Early Infantile Epileptic Encephalopathy, Autosomal Recessive Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs139577104; hg19: chr11-791209;