15-67381230-A-G

Variant names:

• chr15-67381230-A-G
• rs12164949
• NM_001031715.3:c.1373-3706A>G

Variant summary

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

The NM_001031715.3(IQCH):​c.1373-3706A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,030 control chromosomes in the GnomAD database, including 21,775 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 0.53 (21775 hom., cov: 32)
• Consequence: IQCH NM_001031715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 8 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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.1373-3706A>G		intron	N/A	NP_001026885.2	Q86VS3-1
	IQCH	NM_001322475.2		c.854-3706A>G		intron	N/A	NP_001309404.2
	IQCH	NM_001322470.2		c.854-3706A>G		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.1373-3706A>G		intron	N/A	ENSP00000336861.4	Q86VS3-1
	IQCH	ENST00000561357.1	TSL:3	c.209-3706A>G		intron	N/A	ENSP00000457425.1	H3BU17
	IQCH	ENST00000514049.5	TSL:2	n.*962-3706A>G		intron	N/A	ENSP00000421223.1	D6RGG0

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80509 AN: 151912 Hom.: 21746 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.530 AC: 80585 AN: 152030 Hom.: 21775 Cov.: 32 AF XY: 0.536 AC XY: 39820 AN XY: 74302

African (AFR) AF: 0.533 AC: 22094 AN: 41448

American (AMR) AF: 0.642 AC: 9811 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2009 AN: 3466

East Asian (EAS) AF: 0.794 AC: 4104 AN: 5168

South Asian (SAS) AF: 0.674 AC: 3248 AN: 4822

European-Finnish (FIN) AF: 0.473 AC: 5001 AN: 10570

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32533 AN: 67964

Other (OTH) AF: 0.551 AC: 1164 AN: 2112

Alfa AF: 0.504 Hom.: 10621

Bravo AF: 0.544

Asia WGS AF: 0.692 AC: 2403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.71
PhyloP100		-1.2
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: rs12164949; hg19: chr15-67673568;