chr2-86144760-T-A

Variant names:

• chr2-86144760-T-A
• rs8244
• NM_006839.3:c.1785A>T

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_006839.3(IMMT):​c.1785A>T​(p.Ala595Ala) variant causes a synonymous 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)
• Consequence: IMMT NM_006839.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.25
• Publications: 19 publications found

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

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.137).
• BP7: Synonymous conserved (PhyloP=-5.26 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006839.3. 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
	IMMT	NM_006839.3	MANE Select	c.1785A>T	p.Ala595Ala	synonymous	Exon 15 of 15	NP_006830.2	Q16891-1
	IMMT	NM_001100169.2		c.1782A>T	p.Ala594Ala	synonymous	Exon 15 of 15	NP_001093639.1	Q16891-4
	IMMT	NM_001400086.1		c.1779A>T	p.Ala593Ala	synonymous	Exon 15 of 15	NP_001387015.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IMMT	ENST00000410111.8	TSL:1 MANE Select	c.1785A>T	p.Ala595Ala	synonymous	Exon 15 of 15	ENSP00000387262.3	Q16891-1
	IMMT	ENST00000442664.6	TSL:1	c.1782A>T	p.Ala594Ala	synonymous	Exon 15 of 15	ENSP00000407788.2	Q16891-4
	IMMT	ENST00000449247.6	TSL:1	c.1752A>T	p.Ala584Ala	synonymous	Exon 15 of 15	ENSP00000396899.2	Q16891-2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 56

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.18
DANN	Benign	0.58
PhyloP100		-5.3
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=100/0	polymorphism

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: rs8244; hg19: chr2-86371883;