ENST00000509504.2:c.621-488G>A

Variant names:

• chr7-30882505-A-.
• NM_032222.3:c.2152+144A>.

Variant summary

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

The ENST00000509504.2(ENSG00000250424):​c.547+144A>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: ENSG00000250424 ENST00000509504.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

MINDY4 (HGNC:21916): (MINDY lysine 48 deubiquitinase 4) Predicted to enable Lys48-specific deubiquitinase activity. Predicted to be involved in protein K48-linked deubiquitination. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000250424 (HGNC:):

INMT-MINDY4 (HGNC:41995): (INMT-MINDY4 readthrough (NMD candidate)) This locus represents rare but naturally occurring read-through transcription between the INMT (indolethylamine N-methyltransferase) and FAM188B (family with sequence similarity 188, member B) genes on chromosome 7. The read-through transcript is unlikely to produce a protein because it is a nonsense-mediated mRNA decay (NMD) candidate based on translation from the supported INMT start codon. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MINDY4	NM_032222.3	c.2152+144A>.		intron_variant	Intron 16 of 17	ENST00000265299.6	NP_115598.2
INMT-MINDY4	NR_037598.1	n.2681+144A>.		intron_variant	Intron 18 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MINDY4	ENST00000265299.6	c.2152+144A>.		intron_variant	Intron 16 of 17	1	NM_032222.3	ENSP00000265299.6
ENSG00000250424	ENST00000509504.2	c.547+144A>.		intron_variant	Intron 6 of 10	5		ENSP00000421315.2
INMT-MINDY4	ENST00000458257.5	n.*2239+144A>.		intron_variant	Intron 18 of 19	2		ENSP00000456039.1
MINDY4	ENST00000409881.1	n.1985+144A>.		intron_variant	Intron 4 of 5	2

Frequencies

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

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

ClinVar

Not reported in ClinVar

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: chr7-30922120;