rs2367204

chr2-86177288-A-G

Variant summary

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

The NM_006839.3(IMMT):c.309+2145T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.373 in 151,694 control chromosomes in the GnomAD database, including 12,909 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 0.37 (12909 hom., cov: 30)
• Consequence: IMMT NM_006839.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244

Genes affected

IMMT (HGNC:6047): (inner membrane mitochondrial protein) Enables RNA binding activity. Involved in cristae formation. Located in mitochondrial inner membrane. Part of MICOS complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IMMT	NM_006839.3	c.309+2145T>C		intron_variant		ENST00000410111.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IMMT	ENST00000410111.8	c.309+2145T>C		intron_variant		1	NM_006839.3	A1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56606 AN: 151576 Hom.: 12914 Cov.: 30

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.399

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.373 AC: 56589 AN: 151694 Hom.: 12909 Cov.: 30 AF XY: 0.371 AC XY: 27454 AN XY: 74060

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.489

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.397

Alfa AF: 0.447 Hom.: 2142

Bravo AF: 0.354

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	8.0
Dann	Benign	0.41

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: rs2367204; hg19: chr2-86404411;