rs7359257

Positions:

• chr15-67410569-A-C

Variant summary

Our verdict is Benign. Variant got -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

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 = 0.545 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IQCH	NM_001031715.3	c.2098-6362A>C		intron_variant		ENST00000335894.9	NP_001026885.2
IQCH-AS1	NR_040051.1	n.1096-2094T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IQCH	ENST00000335894.9	c.2098-6362A>C		intron_variant		1	NM_001031715.3	ENSP00000336861	A2
IQCH-AS1	ENST00000669759.1	n.121+10766T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.606

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.447

Alfa AF: 0.523 Hom.: 23196

Bravo AF: 0.435

Asia WGS AF: 0.184 AC: 644 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.075
DANN	Benign	0.61

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: rs7359257; hg19: chr15-67702907;