rs7359257

Variant names:

• chr15-67410569-A-C
• rs7359257
• NM_001031715.3:c.2098-6362A>C

Variant summary

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

The NM_001031715.3(IQCH):​c.2098-6362A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,062 control chromosomes in the GnomAD database, including 16,744 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 0.45 (16744 hom., cov: 32)
• Consequence: IQCH NM_001031715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 20 publications found

Genes affected

IQCH (HGNC:25721): (IQ motif containing H)

IQCH-AS1 (HGNC:44104): (IQCH antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031715.3. 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
	IQCH	NM_001031715.3	MANE Select	c.2098-6362A>C		intron	N/A	NP_001026885.2
	IQCH	NM_001322475.2		c.1306-6362A>C		intron	N/A	NP_001309404.2
	IQCH	NM_001322470.2		c.1306-6362A>C		intron	N/A	NP_001309399.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IQCH	ENST00000335894.9	TSL:1 MANE Select	c.2098-6362A>C		intron	N/A	ENSP00000336861.4
	IQCH-AS1	ENST00000561232.5	TSL:1	n.892-2094T>G		intron	N/A
	IQCH	ENST00000514049.5	TSL:2	n.*1414-6362A>C		intron	N/A	ENSP00000421223.1

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68978 AN: 151944 Hom.: 16744 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.454 AC: 68982 AN: 152062 Hom.: 16744 Cov.: 32 AF XY: 0.450 AC XY: 33443 AN XY: 74318

African (AFR) AF: 0.339 AC: 14059 AN: 41496

American (AMR) AF: 0.397 AC: 6052 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1487 AN: 3470

East Asian (EAS) AF: 0.149 AC: 771 AN: 5174

South Asian (SAS) AF: 0.257 AC: 1236 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6410 AN: 10570

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.550 AC: 37357 AN: 67968

Other (OTH) AF: 0.447 AC: 943 AN: 2108

Alfa AF: 0.508 Hom.: 57266

Bravo AF: 0.435

Asia WGS AF: 0.184 AC: 644 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.075
DANN	Benign	0.61
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7359257; hg19: chr15-67702907;