16-21678558-T-G

Variant names:

• chr16-21678558-T-G
• rs78970023
• NM_144672.4:c.44T>G

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_144672.4(OTOA):​c.44T>G​(p.Phe15Cys) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F15Y) has been classified as Benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: OTOA NM_144672.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 23 publications found

Genes affected

OTOA (HGNC:16378): (otoancorin) The protein encoded by this gene is specifically expressed in the inner ear, and is located at the interface between the apical surface of the inner ear sensory epithelia and their overlying acellular gels. It is prposed that this protein is involved in the attachment of the inner ear acellular gels to the apical surface of the underlying nonsensory cells. Mutations in this gene are associated with autosomal recessive deafness type 22 (DFNB22). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

OTOA Gene-Disease associations (from GenCC):

• autosomal recessive nonsyndromic hearing loss 22

  Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Laboratory for Molecular Medicine, G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae)
• nonsyndromic genetic hearing loss

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• hearing loss, autosomal recessive

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.2858285).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OTOA	NM_144672.4	c.44T>G	p.Phe15Cys	missense_variant	Exon 2 of 29	ENST00000646100.2	NP_653273.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OTOA	ENST00000646100.2	c.44T>G	p.Phe15Cys	missense_variant	Exon 2 of 29		NM_144672.4	ENSP00000496564.2
OTOA	ENST00000388958.8	c.44T>G	p.Phe15Cys	missense_variant	Exon 1 of 28	1		ENSP00000373610.3
OTOA	ENST00000286149.8	c.44T>G	p.Phe15Cys	missense_variant	Exon 1 of 28	5		ENSP00000286149.4
OTOA	ENST00000647277.1	n.44T>G		non_coding_transcript_exon_variant	Exon 2 of 29			ENSP00000495594.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Uncertain	0.022	T
BayesDel_noAF	Benign	-0.21
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Benign	0.038	.;T;.
Eigen	Benign	0.067
Eigen_PC	Benign	0.026
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.60	.;T;T
M_CAP	Benign	0.058	D
MetaRNN	Benign	0.29	T;T;T
MetaSVM	Benign	-0.50	T
MutationAssessor	Benign	2.0	M;M;M
PhyloP100		2.4
PrimateAI	Uncertain	0.51	T
PROVEAN	Benign	-1.2	.;N;N
REVEL	Uncertain	0.34
Sift	Uncertain	0.0010	.;D;D
Sift4G	Uncertain	0.0020	.;D;D
Vest4		0.62, 0.64
MutPred		0.36		Gain of catalytic residue at L16 (P = 0.0159);Gain of catalytic residue at L16 (P = 0.0159);Gain of catalytic residue at L16 (P = 0.0159);
MVP		0.82
MPC		0.77
ClinPred		0.84	D
GERP RS		4.7
PromoterAI		0.028	Neutral
Varity_R		0.15
gMVP		0.24

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

Other links and lift over

dbSNP: rs78970023; hg19: chr16-21689879;