4-149439602-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363507.2(IQCM):​c.1229-6045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 151,834 control chromosomes in the GnomAD database, including 11,870 homozygotes. 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: 𝑓 0.38 (11870 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

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>C		intron	N/A	NP_001350436.1
	IQCM	NM_001378177.1		c.1268-6045T>C		intron	N/A	NP_001365106.1
	IQCM	NM_001378178.1		c.1268-6045T>C		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>C		intron	N/A	ENSP00000490518.1
	IQCM	ENST00000511993.5	TSL:1	n.*1108-6045T>C		intron	N/A	ENSP00000490631.1
	IQCM	ENST00000636414.1	TSL:5	c.1229-6045T>C		intron	N/A	ENSP00000490088.1

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57296 AN: 151718 Hom.: 11859 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.378 AC: 57335 AN: 151834 Hom.: 11870 Cov.: 31 AF XY: 0.382 AC XY: 28336 AN XY: 74160

African (AFR) AF: 0.204 AC: 8459 AN: 41472

American (AMR) AF: 0.463 AC: 7052 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1536 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2595 AN: 5134

South Asian (SAS) AF: 0.434 AC: 2088 AN: 4814

European-Finnish (FIN) AF: 0.455 AC: 4776 AN: 10506

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29486 AN: 67910

Other (OTH) AF: 0.414 AC: 872 AN: 2106

Alfa AF: 0.377 Hom.: 1866

Bravo AF: 0.370

Asia WGS AF: 0.478 AC: 1655 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.54
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;