19-54173068-T-A

Position:

• chr19-54173068-T-A

Variant summary

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

The NM_144686.4(TMC4):​c.50A>T​(p.Glu17Val) 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. 6/8 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TMC4 NM_144686.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

TMC4 (HGNC:22998): (transmembrane channel like 4) Predicted to enable mechanosensitive ion channel activity. Predicted to be involved in ion transmembrane transport. Located in extracellular exosome. [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=0.06770602).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMC4	NM_144686.4	c.50A>T	p.Glu17Val	missense_variant	1/15	ENST00000619895.5	NP_653287.2
TMC4	NM_001145303.3	c.50A>T	p.Glu17Val	missense_variant	1/15		NP_001138775.2
TMC4	XM_011526486.3	c.50A>T	p.Glu17Val	missense_variant	1/12		XP_011524788.1
TMC4	XR_935741.3	n.93A>T		non_coding_transcript_exon_variant	1/15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMC4	ENST00000619895.5	c.50A>T	p.Glu17Val	missense_variant	1/15	1	NM_144686.4	ENSP00000479458	P1
TMC4	ENST00000617472.4	c.50A>T	p.Glu17Val	missense_variant	1/15	1		ENSP00000477627
TMC4	ENST00000613492.4	n.93A>T		non_coding_transcript_exon_variant	1/4	3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 52

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.3
DEOGEN2	Benign	0.0092	.;T
LIST_S2	Benign	0.11	T;T
MetaRNN	Benign	0.068	T;T
Sift4G	Uncertain	0.032	D;D
Vest4		0.072
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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

Other links and lift over

dbSNP: rs641738; hg19: chr19-54676763;