Genetic Variant NM_001363538.2:c.2190C>T (chr7-143724382-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001363538.2(TCAF2):c.2190C>T(p.Pro730Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00409 in 1,596,948 control chromosomes in the GnomAD database, including 185 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 75 hom., cov: 20)

Exomes 𝑓: 0.0028 ( 110 hom. )

Consequence

TCAF2
NM_001363538.2 synonymous

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0220

Variant links:

Genes affected

TCAF2 (HGNC:26878): (TRPM8 channel associated factor 2) Enables transmembrane transporter binding activity. Involved in negative regulation of anion channel activity; positive regulation of cell migration; and positive regulation of protein targeting to membrane. Located in cell junction and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

TCAF2 links:

ENSG00000291149 (HGNC:):

ENSG00000291149 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BP6

Variant 7-143724382-C-T is Benign according to our data. Variant chr7-143724382-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 403526.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.022 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.055 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCAF2	NM_001363538.2 link	c.2190C>T	p.Pro730Pro	synonymous_variant	Exon 7 of 8	ENST00000684770.1	NP_001350467.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCAF2	ENST00000684770.1 link	c.2190C>T	p.Pro730Pro	synonymous_variant	Exon 7 of 8		NM_001363538.2	ENSP00000506869.1		A6NFQ2-1

Frequencies

GnomAD3 genomes

AF:

0.0175

AC:

2515

AN:

143446

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0570

Gnomad AMI

AF:

0.00111

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.0154

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000935

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0267

Gnomad NFE

AF:

0.000798

Gnomad OTH

AF:

0.0181

GnomAD3 exomes

AF:

0.00839

AC:

478

AN:

56954

Hom.:

AF XY:

0.00758

AC XY:

218

AN XY:

28742

show subpopulations

Gnomad AFR exome

AF:

0.0626

Gnomad AMR exome

AF:

0.00845

Gnomad ASJ exome

AF:

0.0128

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000495

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00133

Gnomad OTH exome

AF:

0.00573

GnomAD4 exome

AF:

0.00276

AC:

4016

AN:

1453394

Hom.:

110

Cov.:

AF XY:

0.00256

AC XY:

1847

AN XY:

722874

show subpopulations

Gnomad4 AFR exome

AF:

0.0628

Gnomad4 AMR exome

AF:

0.00702

Gnomad4 ASJ exome

AF:

0.0142

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000502

Gnomad4 FIN exome

AF:

0.0000943

Gnomad4 NFE exome

AF:

0.000619

Gnomad4 OTH exome

AF:

0.00734

GnomAD4 genome

AF:

0.0176

AC:

2521

AN:

143554

Hom.:

Cov.:

AF XY:

0.0171

AC XY:

1191

AN XY:

69608

show subpopulations

Gnomad4 AFR

AF:

0.0570

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.0154

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000936

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000798

Gnomad4 OTH

AF:

0.0178

Alfa

AF:

0.0123

Hom.:

Bravo

AF:

0.0215

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent variant not near splice site -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

8.3

DANN

Benign

0.81

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over