Genetic Variant TRIM67:p.Ala166Val (chr1-231163466-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001004342.5(TRIM67):c.497C>T(p.Ala166Val) variant causes a missense 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. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TRIM67
NM_001004342.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.686

Publications

0 publications found

Variant links:

Genes affected

TRIM67 (HGNC:31859): (tripartite motif containing 67) Predicted to enable zinc ion binding activity. Predicted to be involved in regulation of protein localization. Predicted to act upstream of or within negative regulation of Ras protein signal transduction; positive regulation of neuron projection development; and positive regulation of ubiquitin-dependent protein catabolic process. Predicted to be located in cytoplasm and cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

TRIM67 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.058312923).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004342.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM67	NM_001004342.5	MANE Select	c.497C>T	p.Ala166Val	missense	Exon 1 of 10	NP_001004342.3
TRIM67	NM_001410937.1		c.497C>T	p.Ala166Val	missense	Exon 1 of 10	NP_001397866.1	F8W8C1
TRIM67	NM_001300889.3		c.377C>T	p.Ala126Val	missense	Exon 2 of 12	NP_001287818.1	Q6ZTA4-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
TRIM67	ENST00000366653.6	TSL:1 MANE Select	c.497C>T	p.Ala166Val	missense	Exon 1 of 10	ENSP00000355613.5	Q6ZTA4-3
TRIM67	ENST00000449018.7	TSL:1	c.377C>T	p.Ala126Val	missense	Exon 2 of 12	ENSP00000400163.3	Q6ZTA4-2
TRIM67	ENST00000444294.7	TSL:5	c.497C>T	p.Ala166Val	missense	Exon 1 of 10	ENSP00000412124.3	F8W8C1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1383596

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

683760

African (AFR)

AF:

0.00

AC:

AN:

29448

American (AMR)

AF:

0.00

AC:

AN:

36180

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

24816

East Asian (EAS)

AF:

0.00

AC:

AN:

34662

South Asian (SAS)

AF:

0.00

AC:

AN:

77930

European-Finnish (FIN)

AF:

0.00

AC:

AN:

37844

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5370

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1079528

Other (OTH)

AF:

0.00

AC:

AN:

57818

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.33

BayesDel_addAF

Benign

-0.16

BayesDel_noAF

Benign

-0.46

CADD

Benign

(source)

DANN

Benign

0.89

DEOGEN2

Benign

0.0028

Eigen

Benign

-0.75

Eigen_PC

Benign

-0.54

FATHMM_MKL

Benign

0.36

LIST_S2

Uncertain

0.89

M_CAP

Pathogenic

0.44

MetaRNN

Benign

0.058

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.39

PhyloP100

0.69

PrimateAI

Pathogenic

0.81

PROVEAN

Benign

0.090

REVEL

Benign

0.15

Sift

Benign

0.98

Sift4G

Benign

0.49

Polyphen

0.0040

Vest4

0.086

MutPred

0.17

Gain of MoRF binding (P = 0.1042)

MVP

0.082

MPC

0.57

ClinPred

0.10

GERP RS

4.2

PromoterAI

0.037

Neutral

(source)

Varity_R

0.16

gMVP

0.33

Mutation Taster

=87/13

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over