Genetic Variant TMEM196:p.Val23Leu (chr7-19772630-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001363562.2(TMEM196):c.67G>T(p.Val23Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000427 in 1,547,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00022 ( 0 hom., cov: 31)

Exomes 𝑓: 0.000023 ( 0 hom. )

Consequence

TMEM196
NM_001363562.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.51

Variant links:

Genes affected

TMEM196 (HGNC:22431): (transmembrane protein 196) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

TMEM196 links:

LOC107986774 (HGNC:):

LOC107986774 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.0353992).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM196	NM_001363562.2 link	c.67G>T	p.Val23Leu	missense_variant	Exon 1 of 5	ENST00000405844.6	NP_001350491.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
TMEM196	ENST00000405844.6 link	c.67G>T	p.Val23Leu	missense_variant	Exon 1 of 5	5	NM_001363562.2	ENSP00000385087.2	B7WNR7
TMEM196	ENST00000405764.7 link	c.67G>T	p.Val23Leu	missense_variant	Exon 1 of 4	1		ENSP00000384234.3	Q5HYL7-4
TMEM196	ENST00000422233.5 link	c.-58+937G>T		intron_variant	Intron 1 of 4	5		ENSP00000414247.1	F8WE15
TMEM196	ENST00000493519.2 link	c.-58+472G>T		intron_variant	Intron 1 of 3	5		ENSP00000438368.1	Q5HYL7-2

Frequencies

GnomAD3 genomes

AF:

0.000224

AC:

AN:

152070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000749

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.000479

GnomAD3 exomes

AF:

0.0000529

AC:

AN:

151154

Hom.:

AF XY:

0.0000498

AC XY:

AN XY:

80300

show subpopulations

Gnomad AFR exome

AF:

0.00102

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000229

AC:

AN:

1395270

Hom.:

Cov.:

AF XY:

0.0000247

AC XY:

AN XY:

688110

show subpopulations

Gnomad4 AFR exome

AF:

0.000794

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000464

Gnomad4 OTH exome

AF:

0.0000346

GnomAD4 genome

AF:

0.000223

AC:

AN:

152188

Hom.:

Cov.:

AF XY:

0.000255

AC XY:

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.000747

Gnomad4 AMR

AF:

0.0000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.000474

Alfa

AF:

0.000134

Hom.:

Bravo

AF:

0.000280

ExAC

AF:

0.0000786

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Sep 01, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.67G>T (p.V23L) alteration is located in exon 1 (coding exon 1) of the TMEM196 gene. This alteration results from a G to T substitution at nucleotide position 67, causing the valine (V) at amino acid position 23 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.42

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Uncertain

0.99

Eigen

Benign

-0.14

Eigen_PC

Benign

0.087

FATHMM_MKL

Benign

0.64

LIST_S2

Benign

0.83

T;T

M_CAP

Benign

0.0043

MetaRNN

Benign

0.035

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.63

.;N

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-1.5

N;N

REVEL

Benign

0.046

Sift

Benign

0.087

T;T

Sift4G

Benign

0.14

T;T

Polyphen

0.0

.;B

Vest4

0.29

MutPred

0.20

Loss of catalytic residue at V23 (P = 0.2285);Loss of catalytic residue at V23 (P = 0.2285);

MVP

0.19

MPC

0.012

ClinPred

0.086

GERP RS

5.1

gMVP

0.76

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

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