2-110225473-A-G

Variant names:

• chr2-110225473-A-G
• rs10173717
• ENST00000414416.2:c.-967-2534T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000414416.2(MTLN):​c.-967-2534T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 151,886 control chromosomes in the GnomAD database, including 7,613 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 0.30 (7613 hom., cov: 33)
• Consequence: MTLN ENST00000414416.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 3 publications found

Genes affected

MTLN (HGNC:27339): (mitoregulin) Involved in several processes, including fatty acid beta-oxidation; positive regulation of mitochondrial membrane potential; and triglyceride homeostasis. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTLN	ENST00000414416.2	c.-967-2534T>C		intron_variant	Intron 1 of 8	1		ENSP00000485216.1

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45765 AN: 151772 Hom.: 7594 Cov.: 33

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.387

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.302 AC: 45831 AN: 151886 Hom.: 7613 Cov.: 33 AF XY: 0.306 AC XY: 22715 AN XY: 74238

African (AFR) AF: 0.206 AC: 8538 AN: 41518

American (AMR) AF: 0.375 AC: 5722 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3470

East Asian (EAS) AF: 0.561 AC: 2895 AN: 5160

South Asian (SAS) AF: 0.490 AC: 2364 AN: 4822

European-Finnish (FIN) AF: 0.222 AC: 2341 AN: 10530

Middle Eastern (MID) AF: 0.392 AC: 113 AN: 288

European-Non Finnish (NFE) AF: 0.321 AC: 21797 AN: 67840

Other (OTH) AF: 0.312 AC: 657 AN: 2106

Alfa AF: 0.296 Hom.: 1223

Bravo AF: 0.304

Asia WGS AF: 0.480 AC: 1642 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		0.21

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: rs10173717; hg19: chr2-110983050;