rs2654831

Positions:

• chr4-149599732-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363507.2(IQCM):​c.682-11735A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 151,926 control chromosomes in the GnomAD database, including 4,286 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 0.21 (4286 hom., cov: 32)
• Consequence: IQCM NM_001363507.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCM	NM_001363507.2	c.682-11735A>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.682-11735A>C		intron_variant		5	NM_001363507.2	ENSP00000490518	P2
IQCM	ENST00000511993.5	c.*343-11735A>C		intron_variant, NMD_transcript_variant		1		ENSP00000490631
IQCM	ENST00000636414.1	c.682-11735A>C		intron_variant		5		ENSP00000490088	A2
IQCM	ENST00000508106.5	n.697-11735A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32398 AN: 151810 Hom.: 4289 Cov.: 32

Gnomad AFR AF: 0.0682

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.213 AC: 32393 AN: 151926 Hom.: 4286 Cov.: 32 AF XY: 0.214 AC XY: 15867 AN XY: 74210

Gnomad4 AFR AF: 0.0683

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.229

Alfa AF: 0.244 Hom.: 1675

Bravo AF: 0.198

Asia WGS AF: 0.143 AC: 498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2654831; hg19: chr4-150520884;