NM_001257308.2:c.84C>A

Variant names:

• chr5-129748274-C-A
• NM_001257308.2:c.84C>A
• MINAR2 p.Ala28Ala

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001257308.2(MINAR2):​c.84C>A​(p.Ala28Ala) variant causes a synonymous 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. Synonymous variant affecting the same amino acid position (i.e. A28A) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MINAR2 NM_001257308.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 0 publications found

Genes affected

MINAR2 (HGNC:33914): (membrane integral NOTCH2 associated receptor 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MINAR2 Gene-Disease associations (from GenCC):

• hearing loss, autosomal recessive 120

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

CHSY3-AS1 (HGNC:58253):

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP7: Synonymous conserved (PhyloP=-0.322 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001257308.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINAR2	NM_001257308.2	MANE Select	c.84C>A	p.Ala28Ala	synonymous	Exon 1 of 3	NP_001244237.1	P59773

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MINAR2	ENST00000564719.2	TSL:5 MANE Select	c.84C>A	p.Ala28Ala	synonymous	Exon 1 of 3	ENSP00000454268.1	P59773
	CHSY3-AS1	ENST00000503616.5	TSL:3	n.285-13212G>T		intron	N/A
	CHSY3-AS1	ENST00000653455.2		n.313-13212G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	4.2
DANN	Benign	0.85
PhyloP100		-0.32
PromoterAI		-0.026	Neutral

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr5-129083967;