rs6494654

Variant names:

• chr15-67389569-T-A
• rs6494654
• NM_001031715.3:c.1632+563T>A

Your query was ambiguous. Multiple possible variants found:

• chr15-67389569-T-A
• chr15-67389569-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001031715.3(IQCH):​c.1632+563T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCH	NM_001031715.3	c.1632+563T>A		intron_variant	Intron 12 of 20	ENST00000335894.9	NP_001026885.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCH	ENST00000335894.9	c.1632+563T>A		intron_variant	Intron 12 of 20	1	NM_001031715.3	ENSP00000336861.4
IQCH	ENST00000561357.1	c.468+563T>A		intron_variant	Intron 4 of 4	3		ENSP00000457425.1
IQCH	ENST00000514049.5	n.*1221+563T>A		intron_variant	Intron 10 of 16	2		ENSP00000421223.1
IQCH-AS1	ENST00000669759.1	n.121+31766A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 84537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.1
DANN	Benign	0.49
PhyloP100		-0.038

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;