chr15-72398343-A-C

Position:

• chr15-72398343-A-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001080462.3(TMEM202):​c.17A>C​(p.His6Pro) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TMEM202 NM_001080462.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.363

Genes affected

TMEM202 (HGNC:33733): (transmembrane protein 202) Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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=0.065375626).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM202	NM_001080462.3	c.17A>C	p.His6Pro	missense_variant	1/5	ENST00000341689.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM202	ENST00000341689.4	c.17A>C	p.His6Pro	missense_variant	1/5	5	NM_001080462.3	P1
TMEM202	ENST00000567679.1	c.17A>C	p.His6Pro	missense_variant	1/3	2
TMEM202	ENST00000649825.1	c.-131A>C		5_prime_UTR_variant	1/5
TMEM202	ENST00000568167.5	c.17A>C	p.His6Pro	missense_variant, NMD_transcript_variant	1/4	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 09, 2023

The c.17A>C (p.H6P) alteration is located in exon 1 (coding exon 1) of the TMEM202 gene. This alteration results from a A to C substitution at nucleotide position 17, causing the histidine (H) at amino acid position 6 to be replaced by a proline (P). 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
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.27	T
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.2
DANN	Benign	0.55
DEOGEN2	Benign	0.012	T;.
Eigen	Benign	-0.92
Eigen_PC	Benign	-0.94
FATHMM_MKL	Benign	0.0099	N
LIST_S2	Benign	0.42	T;T
M_CAP	Benign	0.0052	T
MetaRNN	Benign	0.065	T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.76	N;.
MutationTaster	Benign	1.0	N;N
PrimateAI	Benign	0.37	T
PROVEAN	Benign	-1.4	N;D
REVEL	Benign	0.049
Sift	Benign	0.12	T;D
Sift4G	Benign	0.32	T;T
Polyphen		0.0	B;.
Vest4		0.14
MutPred		0.12		Gain of glycosylation at H6 (P = 0.0297);Gain of glycosylation at H6 (P = 0.0297);
MVP		0.055
MPC		0.15
ClinPred		0.070	T
GERP RS		1.6
Varity_R		0.14
gMVP		0.016

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-72690684;