chr1-235109864-G-A

Variant names:

• chr1-235109864-G-A
• rs11301
• NM_014765.3:c.*2200C>T

Variant summary

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

The NM_014765.3(TOMM20):​c.*2200C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,122 control chromosomes in the GnomAD database, including 39,012 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 0.71 (39011 hom., cov: 32)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: TOMM20 NM_014765.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 16 publications found

Genes affected

TOMM20 (HGNC:20947): (translocase of outer mitochondrial membrane 20) Enables protein-transporting ATPase activity and unfolded protein binding activity. Involved in protein targeting to mitochondrion. Located in mitochondria-associated endoplasmic reticulum membrane and mitochondrial outer membrane. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014765.3. 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
	TOMM20	NM_014765.3	MANE Select	c.*2200C>T		3_prime_UTR	Exon 5 of 5	NP_055580.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TOMM20	ENST00000366607.5	TSL:1 MANE Select	c.*2200C>T		3_prime_UTR	Exon 5 of 5	ENSP00000355566.4
	TOMM20	ENST00000932122.1		c.*2200C>T		3_prime_UTR	Exon 5 of 5	ENSP00000602181.1
	TOMM20	ENST00000932121.1		c.*2200C>T		3_prime_UTR	Exon 5 of 5	ENSP00000602180.1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107692 AN: 152000 Hom.: 38977 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.682

Gnomad FIN AF: 0.731

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.663

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AF: 1.00 AC: 2 AN: 2

GnomAD4 genome AF: 0.709 AC: 107779 AN: 152118 Hom.: 39011 Cov.: 32 AF XY: 0.708 AC XY: 52669 AN XY: 74352

African (AFR) AF: 0.838 AC: 34778 AN: 41508

American (AMR) AF: 0.646 AC: 9861 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2352 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2072 AN: 5188

South Asian (SAS) AF: 0.682 AC: 3289 AN: 4824

European-Finnish (FIN) AF: 0.731 AC: 7713 AN: 10558

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.671 AC: 45632 AN: 67986

Other (OTH) AF: 0.657 AC: 1385 AN: 2108

Alfa AF: 0.670 Hom.: 40929

Bravo AF: 0.702

Asia WGS AF: 0.566 AC: 1972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.29
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs11301; hg19: chr1-235273179;