rs116525996

Variant names:

• chr5-110738696-T-A
• rs116525996
• NM_001303250.3:c.10+449T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-110738696-T-A
• chr5-110738696-T-C

Variant summary

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

The NM_001303250.3(SLC25A46):​c.10+449T>A variant causes a intron 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: SLC25A46 NM_001303250.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 0 publications found

Genes affected

SLC25A46 (HGNC:25198): (solute carrier family 25 member 46) This gene encodes a mitochondrial solute carrier protein family member. It functions in promoting mitochondrial fission, and prevents the formation of hyperfilamentous mitochondria. Mutation of this gene results in neuropathy and optic atrophy. [provided by RefSeq, Aug 2016]

TMEM232 (HGNC:37270): (transmembrane protein 232) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC25A46	NM_001303250.3	c.10+449T>A		intron_variant	Intron 1 of 7		NP_001290179.1
TMEM232	XM_006714670.4	c.-298+26A>T		intron_variant	Intron 1 of 15		XP_006714733.1
TMEM232	XM_011543552.3	c.-649+26A>T		intron_variant	Intron 1 of 16		XP_011541854.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC25A46	ENST00000513807.5	c.-204+449T>A		intron_variant	Intron 1 of 7	2		ENSP00000421134.1
TMEM232	ENST00000515278.6	c.-298+26A>T		intron_variant	Intron 1 of 6	5		ENSP00000421614.2
TMEM232	ENST00000503527.6	n.197+26A>T		intron_variant	Intron 1 of 3	3
SLC25A46	ENST00000508781.5	n.112+449T>A		intron_variant	Intron 1 of 7	4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 76858 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 40698

African (AFR) AF: 0.00 AC: 0 AN: 850

American (AMR) AF: 0.00 AC: 0 AN: 2056

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2054

East Asian (EAS) AF: 0.00 AC: 0 AN: 1022

South Asian (SAS) AF: 0.00 AC: 0 AN: 13630

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4860

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 47526

Other (OTH) AF: 0.00 AC: 0 AN: 4546

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 4

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.2
DANN	Benign	0.61
PhyloP100		-0.075
PromoterAI		0.030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs116525996; hg19: chr5-110074397;