rs7521237

Variant names:

• chr1-180926021-A-T
• rs7521237
• NM_020950.2:c.1062-2409A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020950.2(KIAA1614):​c.1062-2409A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 152,218 control chromosomes in the GnomAD database, including 332 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 0.044 (332 hom., cov: 32)
• Consequence: KIAA1614 NM_020950.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.134
• Publications: 1 publications found

Genes affected

KIAA1614 (HGNC:29327): (KIAA1614) Predicted to enable protein kinase C binding activity. Predicted to be involved in centrosome cycle; establishment or maintenance of cell polarity; and regulation of cellular localization. Predicted to be active in apical plasma membrane; cell cortex; and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020950.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1614	NM_020950.2	MANE Select	c.1062-2409A>T		intron	N/A	NP_066001.1	Q5VZ46-1
	KIAA1614	NM_001427641.1		c.1062-2409A>T		intron	N/A	NP_001414570.1	A0AAQ5BGH9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1614	ENST00000367588.9	TSL:1 MANE Select	c.1062-2409A>T		intron	N/A	ENSP00000356560.4	Q5VZ46-1
	KIAA1614	ENST00000713624.1		c.1062-2409A>T		intron	N/A	ENSP00000518922.1	A0AAQ5BGH9
	KIAA1614	ENST00000713623.1		c.1062-2409A>T		intron	N/A	ENSP00000518921.1	A0AAQ5BGG4

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6744 AN: 152100 Hom.: 331 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0260

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.0322

Gnomad FIN AF: 0.00396

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.0450

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

GnomAD4 genome AF: 0.0444 AC: 6760 AN: 152218 Hom.: 332 Cov.: 32 AF XY: 0.0433 AC XY: 3225 AN XY: 74430

African (AFR) AF: 0.124 AC: 5161 AN: 41520

American (AMR) AF: 0.0216 AC: 331 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0260 AC: 90 AN: 3468

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5182

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4816

European-Finnish (FIN) AF: 0.00396 AC: 42 AN: 10610

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 861 AN: 68014

Other (OTH) AF: 0.0445 AC: 94 AN: 2110

Alfa AF: 0.0320 Hom.: 33

Bravo AF: 0.0491

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.67
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

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: rs7521237; hg19: chr1-180895157;