chr15-57633724-A-C

Position:

• chr15-57633724-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001018100.5(MYZAP):​c.916A>C​(p.Ile306Leu) 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: MYZAP NM_001018100.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.17

Genes affected

MYZAP (HGNC:43444): (myocardial zonula adherens protein) This gene encodes a protein that is abundantly expressed in cardiac tissue. The encoded protein localizes to intercalated discs in cardiomyocytes and functions as an activator of Rho-dependent serum-response factor signaling. Alternative splicing results in multiple transcript variants. Readthrough transcription also exists between this gene and the neighboring downstream gene POLR2M (polymerase (RNA) II (DNA directed) polypeptide M) and is represented with GeneID: 145781. [provided by RefSeq, Mar 2014]

GCOM1 (HGNC:26424): (GCOM1, MYZAP-POLR2M combined locus) This locus represents naturally occurring readthrough transcription between the neighboring MYZAP (myocardial zonula adherens protein) and POLR2M (polymerase (RNA) II (DNA directed) polypeptide M) genes on chromosome 15. Alternative splicing results in multiple readthrough transcript variants. Readthrough variants may encode proteins that share sequence identity with the upstream gene product or with both the upstream and downstream gene products. Some readthrough transcript variants are also expected to be candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Oct 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.068519056).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYZAP	NM_001018100.5	c.916A>C	p.Ile306Leu	missense_variant	8/13	ENST00000267853.10
GCOM1	NR_104367.2	n.1047A>C		non_coding_transcript_exon_variant	8/16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MYZAP	ENST00000267853.10	c.916A>C	p.Ile306Leu	missense_variant	8/13	1	NM_001018100.5	P1
MYZAP	ENST00000380565.8	c.916A>C	p.Ile306Leu	missense_variant	8/12	1
GCOM1	ENST00000649429.1	c.916A>C	p.Ile306Leu	missense_variant	8/11
MYZAP	ENST00000461709.1	c.61A>C	p.Ile21Leu	missense_variant	1/5	3

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

Inborn genetic diseases Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Dec 08, 2023

The c.916A>C (p.I306L) alteration is located in exon 8 (coding exon 8) of the GCOM1 gene. This alteration results from a A to C substitution at nucleotide position 916, causing the isoleucine (I) at amino acid position 306 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
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	21
DANN	Benign	0.97
DEOGEN2	Benign	0.0052	.;.;.;.;T;.;.
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.054
FATHMM_MKL	Benign	0.73	D
LIST_S2	Uncertain	0.88	D;D;.;D;D;D;T
M_CAP	Benign	0.0070	T
MetaRNN	Benign	0.069	T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.23	.;.;.;.;N;N;.
MutationTaster	Benign	0.87	D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-0.25	N;.;.;N;N;N;N
REVEL	Benign	0.11
Sift	Benign	0.55	T;.;.;T;T;T;T
Sift4G	Benign	0.81	T;T;.;T;T;T;D
Polyphen		0.0090, 0.63	.;.;.;.;B;P;.
Vest4		0.37
MutPred		0.076		Loss of MoRF binding (P = 0.1167);Loss of MoRF binding (P = 0.1167);Loss of MoRF binding (P = 0.1167);Loss of MoRF binding (P = 0.1167);Loss of MoRF binding (P = 0.1167);Loss of MoRF binding (P = 0.1167);.;
MVP		0.40
MPC		0.041
ClinPred		0.39	T
GERP RS		4.6
Varity_R		0.086
gMVP		0.36

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: chr15-57925922;