1-180926021-A-T

Position:

• chr1-180926021-A-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1614	NM_020950.2	c.1062-2409A>T		intron_variant		ENST00000367588.9	NP_066001.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1614	ENST00000367588.9	c.1062-2409A>T		intron_variant		1	NM_020950.2	ENSP00000356560.4

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0260

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.0326

Gnomad4 FIN AF: 0.00396

Gnomad4 NFE AF: 0.0127

Gnomad4 OTH AF: 0.0445

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.67

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: rs7521237; hg19: chr1-180895157;