rs10030601

chr4-149804060-T-C

Variant summary

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

The NM_001363507.2(IQCM):c.-49+11251A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 151,720 control chromosomes in the GnomAD database, including 6,535 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 0.22 (6535 hom., cov: 32)
• Consequence: IQCM NM_001363507.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQCM	NM_001363507.2	c.-49+11251A>G		intron_variant		ENST00000636793.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCM	ENST00000636793.2	c.-49+11251A>G		intron_variant		5	NM_001363507.2	P2

Frequencies

GnomAD3 genomes AF: 0.220 AC: 33322 AN: 151602 Hom.: 6507 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.220 AC: 33398 AN: 151720 Hom.: 6535 Cov.: 32 AF XY: 0.229 AC XY: 17000 AN XY: 74132

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.0476

Gnomad4 OTH AF: 0.192

Alfa AF: 0.144 Hom.: 486

Bravo AF: 0.236

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10030601; hg19: chr4-150725212;