chr22-19177322-A-T

Variant names:

• chr22-19177322-A-T
• rs3213491
• NM_005984.5:c.442-118T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_005984.5(SLC25A1):​c.442-118T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000147 in 678,982 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000015 (0 hom.)
• Consequence: SLC25A1 NM_005984.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.883
• Publications: 0 publications found

Genes affected

SLC25A1 (HGNC:10979): (solute carrier family 25 member 1) This gene encodes a member of the mitochondrial carrier subfamily of solute carrier proteins. Members of this family include nuclear-encoded transporters that translocate small metabolites across the mitochondrial membrane. This protein regulates the movement of citrate across the inner membranes of the mitochondria. Mutations in this gene have been associated with combined D-2- and L-2-hydroxyglutaric aciduria. Pseudogenes of this gene have been identified on chromosomes 7, 11, 16, and 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2013]

LINC01311 (HGNC:50503): (long intergenic non-protein coding RNA 1311)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A1	NM_005984.5	c.442-118T>A		intron_variant	Intron 4 of 8	ENST00000215882.10	NP_005975.1
SLC25A1	NM_001256534.2	c.463-118T>A		intron_variant	Intron 3 of 7		NP_001243463.1
SLC25A1	NM_001287387.2	c.133-118T>A		intron_variant	Intron 4 of 8		NP_001274316.1
SLC25A1	NR_046298.3	n.366-118T>A		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A1	ENST00000215882.10	c.442-118T>A		intron_variant	Intron 4 of 8	1	NM_005984.5	ENSP00000215882.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000147 AC: 1 AN: 678982 Hom.: 0 AF XY: 0.00000286 AC XY: 1 AN XY: 350152

African (AFR) AF: 0.00 AC: 0 AN: 17134

American (AMR) AF: 0.00 AC: 0 AN: 26494

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16626

East Asian (EAS) AF: 0.00 AC: 0 AN: 32236

South Asian (SAS) AF: 0.0000179 AC: 1 AN: 55904

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44664

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3848

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 448552

Other (OTH) AF: 0.00 AC: 0 AN: 33524

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.5
DANN	Benign	0.78
PhyloP100		-0.88

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

Other links and lift over

dbSNP: rs3213491; hg19: chr22-19164835;