15-67389569-T-C

Variant names:

• chr15-67389569-T-C
• rs6494654
• NM_001031715.3:c.1632+563T>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.1632+563T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 151,844 control chromosomes in the GnomAD database, including 15,873 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 0.44 (15873 hom., cov: 30)
• Consequence: IQCH NM_001031715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 2 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 = 0.533 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.1632+563T>C		intron	N/A	NP_001026885.2	Q86VS3-1
	IQCH	NM_001322475.2		c.1113+563T>C		intron	N/A	NP_001309404.2
	IQCH	NM_001322470.2		c.1113+563T>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.1632+563T>C		intron	N/A	ENSP00000336861.4	Q86VS3-1
	IQCH	ENST00000561357.1	TSL:3	c.468+563T>C		intron	N/A	ENSP00000457425.1	H3BU17
	IQCH	ENST00000514049.5	TSL:2	n.*1221+563T>C		intron	N/A	ENSP00000421223.1	D6RGG0

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67060 AN: 151726 Hom.: 15872 Cov.: 30

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.584

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.442 AC: 67066 AN: 151844 Hom.: 15873 Cov.: 30 AF XY: 0.437 AC XY: 32449 AN XY: 74200

African (AFR) AF: 0.327 AC: 13535 AN: 41396

American (AMR) AF: 0.384 AC: 5862 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1451 AN: 3466

East Asian (EAS) AF: 0.150 AC: 777 AN: 5178

South Asian (SAS) AF: 0.248 AC: 1191 AN: 4810

European-Finnish (FIN) AF: 0.584 AC: 6137 AN: 10510

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36539 AN: 67920

Other (OTH) AF: 0.433 AC: 912 AN: 2106

Alfa AF: 0.493 Hom.: 84537

Bravo AF: 0.423

Asia WGS AF: 0.181 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.43
PhyloP100		-0.038
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: rs6494654; hg19: chr15-67681907;