Genetic Variant NM_001363507.2:c.1229-42280dupT (chr4-149475836-C-CA) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001363507.2(IQCM):c.1229-42280dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

IQCM
NM_001363507.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378

Publications

1 publications found

Variant links:

Genes affected

IQCM (HGNC:53443): (IQ motif containing M)

IQCM links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363507.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IQCM	NM_001363507.2	MANE Select	c.1229-42280dupT	intron	N/A	NP_001350436.1
IQCM	NM_001378177.1		c.1268-42280dupT	intron	N/A	NP_001365106.1
IQCM	NM_001378178.1		c.1268-42280dupT	intron	N/A	NP_001365107.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IQCM	ENST00000636793.2	TSL:5 MANE Select	c.1229-42280dupT	intron	N/A	ENSP00000490518.1
IQCM	ENST00000511993.5	TSL:1	n.*1107+38688dupT	intron	N/A	ENSP00000490631.1
IQCM	ENST00000636414.1	TSL:5	c.1229-42280dupT	intron	N/A	ENSP00000490088.1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over