rs8038652

chr15-67259726-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001031715.3(IQCH):c.52-1546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,244 control chromosomes in the GnomAD database, including 4,409 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 0.23 (4409 hom., cov: 33)
• Consequence: IQCH NM_001031715.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IQCH	NM_001031715.3	c.52-1546G>A		intron_variant		ENST00000335894.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IQCH	ENST00000335894.9	c.52-1546G>A		intron_variant		1	NM_001031715.3	A2

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34262 AN: 152126 Hom.: 4394 Cov.: 33

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.225 AC: 34315 AN: 152244 Hom.: 4409 Cov.: 33 AF XY: 0.229 AC XY: 17081 AN XY: 74430

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.266

Alfa AF: 0.222 Hom.: 745

Bravo AF: 0.234

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	7.6
Dann	Benign	0.60

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: rs8038652; hg19: chr15-67552064;