1-161226376-A-T

Variant names:

• chr1-161226376-A-T
• rs3813628
• NM_032174.6:c.-114A>T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_032174.6(TOMM40L):​c.-114A>T variant causes a 5 prime UTR 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: 27)
• Consequence: TOMM40L NM_032174.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 16 publications found

Genes affected

TOMM40L (HGNC:25756): (translocase of outer mitochondrial membrane 40 like) Predicted to enable protein transmembrane transporter activity. Predicted to be involved in protein import into mitochondrial matrix. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032174.6. 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
	TOMM40L	NM_032174.6	MANE Select	c.-114A>T		5_prime_UTR	Exon 2 of 10	NP_115550.2
	TOMM40L	NM_001286373.2		c.-114A>T		5_prime_UTR	Exon 2 of 9	NP_001273302.1	Q969M1-2
	TOMM40L	NM_001286374.2		c.-114A>T		5_prime_UTR	Exon 2 of 8	NP_001273303.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOMM40L	ENST00000367988.8	TSL:2 MANE Select	c.-114A>T		5_prime_UTR	Exon 2 of 10	ENSP00000356967.3	Q969M1-1
	TOMM40L	ENST00000367987.1	TSL:1	c.-114A>T		5_prime_UTR	Exon 1 of 9	ENSP00000356966.1	Q969M1-1
	TOMM40L	ENST00000951902.1		c.-114A>T		5_prime_UTR	Exon 2 of 10	ENSP00000621961.1

Frequencies

GnomAD3 genomes Cov.: 27

GnomAD4 exome Cov.: 10

GnomAD4 genome Cov.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	19
DANN	Benign	0.89
PhyloP100		1.9
PromoterAI		0.014	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.23		Position offset: -21

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

Other links and lift over

dbSNP: rs3813628; hg19: chr1-161196166;