4-149439602-A-G

Position:

• chr4-149439602-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCM	NM_001363507.2	c.1229-6045T>C		intron_variant		ENST00000636793.2	NP_001350436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQCM	ENST00000636793.2	c.1229-6045T>C		intron_variant		5	NM_001363507.2	ENSP00000490518	P2
IQCM	ENST00000511993.5	c.*1108-6045T>C		intron_variant, NMD_transcript_variant		1		ENSP00000490631
IQCM	ENST00000636414.1	c.1229-6045T>C		intron_variant		5		ENSP00000490088	A2

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

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.505

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.414

Alfa AF: 0.382 Hom.: 1856

Bravo AF: 0.370

Asia WGS AF: 0.478 AC: 1655 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7668351; hg19: chr4-150360754;