rs10030601

Variant names:

• chr4-149804060-T-C
• rs10030601
• NM_001363507.2:c.-49+11251A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCM	NM_001363507.2	MANE Select	c.-49+11251A>G		intron	N/A	NP_001350436.1	A0A1B0GVH7
	IQCM	NM_001378177.1		c.-112+11251A>G		intron	N/A	NP_001365106.1
	IQCM	NM_001378178.1		c.-49+11251A>G		intron	N/A	NP_001365107.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCM	ENST00000636793.2	TSL:5 MANE Select	c.-49+11251A>G		intron	N/A	ENSP00000490518.1	A0A1B0GVH7
	IQCM	ENST00000511993.5	TSL:1	n.-112+11251A>G		intron	N/A	ENSP00000490631.1	A0A1B0GVS1
	IQCM	ENST00000636414.1	TSL:5	c.-49+11251A>G		intron	N/A	ENSP00000490088.1	A0A1B0GUF7

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

African (AFR) AF: 0.495 AC: 20494 AN: 41370

American (AMR) AF: 0.267 AC: 4053 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 450 AN: 3460

East Asian (EAS) AF: 0.372 AC: 1908 AN: 5128

South Asian (SAS) AF: 0.186 AC: 893 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1903 AN: 10568

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0476 AC: 3235 AN: 67898

Other (OTH) AF: 0.192 AC: 405 AN: 2108

Alfa AF: 0.158 Hom.: 576

Bravo AF: 0.236

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10030601; hg19: chr4-150725212;