4-149439602-A-C

Variant names:

• chr4-149439602-A-C
• rs7668351
• NM_001363507.2:c.1229-6045T>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001363507.2(IQCM):​c.1229-6045T>G variant causes a intron 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.

• Frequency: Genomes: not found (cov: 31)
• Consequence: IQCM NM_001363507.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCM	NM_001363507.2	MANE Select	c.1229-6045T>G		intron	N/A	NP_001350436.1
	IQCM	NM_001378177.1		c.1268-6045T>G		intron	N/A	NP_001365106.1
	IQCM	NM_001378178.1		c.1268-6045T>G		intron	N/A	NP_001365107.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCM	ENST00000636793.2	TSL:5 MANE Select	c.1229-6045T>G		intron	N/A	ENSP00000490518.1
	IQCM	ENST00000511993.5	TSL:1	n.*1108-6045T>G		intron	N/A	ENSP00000490631.1
	IQCM	ENST00000636414.1	TSL:5	c.1229-6045T>G		intron	N/A	ENSP00000490088.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.52
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7668351; hg19: chr4-150360754;