rs7198

Variant names:

• chr17-75273177-G-A
• rs7198
• NM_001126121.2:c.*274C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-75273177-G-A
• chr17-75273177-G-C
• chr17-75273177-G-T

Variant summary

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

The NM_021734.5(SLC25A19):​c.*274C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC25A19 NM_021734.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833
• Publications: 8 publications found

Genes affected

SLC25A19 (HGNC:14409): (solute carrier family 25 member 19) This gene encodes a mitochondrial protein that is a member of the solute carrier family. Although this protein was initially thought to be the mitochondrial deoxynucleotide carrier involved in the uptake of deoxynucleotides into the matrix of the mitochondria, further studies have demonstrated that this protein instead functions as the mitochondrial thiamine pyrophosphate carrier, which transports thiamine pyrophosphates into mitochondria. Mutations in this gene cause microcephaly, Amish type, a metabolic disease that results in severe congenital microcephaly, severe 2-ketoglutaric aciduria, and death within the first year. Multiple alternatively spliced variants, encoding the same protein, have been identified for this gene. [provided by RefSeq, Jul 2008]

MIF4GD-DT (HGNC:55335): (MIF4GD divergent transcript)

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=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021734.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A19	NM_001126121.2	MANE Select	c.*274C>T		3_prime_UTR	Exon 8 of 8	NP_001119593.1
	SLC25A19	NM_001126122.2		c.*274C>T		3_prime_UTR	Exon 7 of 7	NP_001119594.1
	SLC25A19	NM_021734.5		c.*274C>T		3_prime_UTR	Exon 8 of 8	NP_068380.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC25A19	ENST00000416858.7	TSL:1 MANE Select	c.*274C>T		3_prime_UTR	Exon 8 of 8	ENSP00000397818.2
	SLC25A19	ENST00000402418.7	TSL:1	c.*274C>T		3_prime_UTR	Exon 6 of 6	ENSP00000385312.3
	SLC25A19	ENST00000320362.7	TSL:2	c.*274C>T		3_prime_UTR	Exon 9 of 9	ENSP00000319574.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 324892 Hom.: 0 Cov.: 2 AF XY: 0.00 AC XY: 0 AN XY: 172668

African (AFR) AF: 0.00 AC: 0 AN: 9706

American (AMR) AF: 0.00 AC: 0 AN: 14414

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9840

East Asian (EAS) AF: 0.00 AC: 0 AN: 19704

South Asian (SAS) AF: 0.00 AC: 0 AN: 43328

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16838

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1422

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 191174

Other (OTH) AF: 0.00 AC: 0 AN: 18466

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		-0.83

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: rs7198; hg19: chr17-73269258;