NM_153208.3:c.803-6504T>C

Variant names:

• chr16-19849983-T-C
• rs227761
• NM_153208.3:c.803-6504T>C

Variant summary

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

The NM_153208.3(IQCK):​c.803-6504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,992 control chromosomes in the GnomAD database, including 30,252 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 0.61 (30252 hom., cov: 31)
• Consequence: IQCK NM_153208.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.480

Genes affected

IQCK (HGNC:28556): (IQ motif containing K) This gene belongs to the IQ motif-containing family of proteins. The IQ motif serves as a binding site for different EF-hand proteins such as calmodulin. This gene was identified as a potential candidate gene for obsessive-compulsive disorder in a genome-wide association study. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IQCK	NM_153208.3	c.803-6504T>C		intron_variant	Intron 8 of 8	ENST00000695302.1	NP_694940.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IQCK	ENST00000695302.1	c.803-6504T>C		intron_variant	Intron 8 of 8		NM_153208.3	ENSP00000511791.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92403 AN: 151874 Hom.: 30211 Cov.: 31

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.634

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.609 AC: 92494 AN: 151992 Hom.: 30252 Cov.: 31 AF XY: 0.611 AC XY: 45386 AN XY: 74308

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.847

Gnomad4 SAS AF: 0.634

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.614

Alfa AF: 0.519 Hom.: 30693

Bravo AF: 0.631

Asia WGS AF: 0.753 AC: 2616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.86
DANN	Benign	0.40

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: rs227761; hg19: chr16-19861305;