rs2285647

Positions:

• chr7-87837656-G-A
• chr7-87837656-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018843.4(SLC25A40):​c.824-846C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 150,580 control chromosomes in the GnomAD database, including 5,789 homozygotes. 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: 𝑓 0.27 (5789 hom., cov: 30)
• Consequence: SLC25A40 NM_018843.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

Genes affected

SLC25A40 (HGNC:29680): (solute carrier family 25 member 40) SLC25A40 belongs to the SLC25 family of mitochondrial carrier proteins (Haitina et al., 2006 [PubMed 16949250]).[supplied by OMIM, Mar 2008]

SLC25A40 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC25A40	NM_018843.4	c.824-846C>T		intron_variant		ENST00000341119.10	NP_061331.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC25A40	ENST00000341119.10	c.824-846C>T		intron_variant		1	NM_018843.4	ENSP00000344831.5

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41322 AN: 150462 Hom.: 5785 Cov.: 30

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.275 AC: 41346 AN: 150580 Hom.: 5789 Cov.: 30 AF XY: 0.270 AC XY: 19831 AN XY: 73534

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.280

Alfa AF: 0.283 Hom.: 8300

Bravo AF: 0.270

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.1
DANN	Benign	0.45

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: rs2285647; hg19: chr7-87466971;