chr5-129764899-CTGCGGTTT-C

Variant names:

• chr5-129764899-CTGCGGTTT-C
• NM_001257308.2:c.412_419delCGGTTTTG

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_Strong PM2 PP5

The NM_001257308.2(MINAR2):​c.412_419delCGGTTTTG​(p.Arg138ValfsTer10) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MINAR2 NM_001257308.2 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 5.12

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]

ENSG00000251680 (HGNC:58253):

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.281 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 5-129764899-CTGCGGTTT-C is Pathogenic according to our data. Variant chr5-129764899-CTGCGGTTT-C is described in ClinVar as [Pathogenic]. Clinvar id is 2443701.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MINAR2	NM_001257308.2	c.412_419delCGGTTTTG	p.Arg138ValfsTer10	frameshift_variant	Exon 3 of 3	ENST00000564719.2	NP_001244237.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MINAR2	ENST00000564719.2	c.412_419delCGGTTTTG	p.Arg138ValfsTer10	frameshift_variant	Exon 3 of 3	5	NM_001257308.2	ENSP00000454268.1
ENSG00000251680	ENST00000503616.5	n.122-2238_122-2231delAAACCGCA		intron_variant	Intron 2 of 4	3
ENSG00000251680	ENST00000515569.1	n.286-2238_286-2231delAAACCGCA		intron_variant	Intron 3 of 3	2
ENSG00000251680	ENST00000653455.1	n.94-2238_94-2231delAAACCGCA		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Hearing loss, autosomal recessive 120 Pathogenic:1

Feb 08, 2023

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Computational scores

Source: dbNSFP v4.3

Splicing

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: chr5-129100592;