rs35646470

Variant names:

• chr4-149475836-C-CA
• rs35646470
• NM_001363507.2:c.1229-42280dupT

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.378
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCM	NM_001363507.2	c.1229-42280dupT		intron_variant	Intron 12 of 13	ENST00000636793.2	NP_001350436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCM	ENST00000636793.2	c.1229-42280dupT		intron_variant	Intron 12 of 13	5	NM_001363507.2	ENSP00000490518.1
IQCM	ENST00000511993.5	n.*1107+38688dupT		intron_variant	Intron 15 of 16	1		ENSP00000490631.1
IQCM	ENST00000636414.1	c.1229-42280dupT		intron_variant	Intron 12 of 13	5		ENSP00000490088.1

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

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs35646470; hg19: chr4-150396988;