15-67389569-T-C

Position:

• chr15-67389569-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQCH	NM_001031715.3	c.1632+563T>C		intron_variant		ENST00000335894.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCH	ENST00000335894.9	c.1632+563T>C		intron_variant		1	NM_001031715.3	A2
IQCH-AS1	ENST00000669759.1	n.121+31766A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.584

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.433

Alfa AF: 0.502 Hom.: 40977

Bravo AF: 0.423

Asia WGS AF: 0.181 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.8
DANN	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494654; hg19: chr15-67681907;