rs12414014

chr10-24233901-G-Achr10-24233901-G-T

Variant summary

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

The NM_019590.5(KIAA1217):c.354+13992G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 151,844 control chromosomes in the GnomAD database, including 5,450 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 0.25 (5450 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

Genes affected

KIAA1217 (HGNC:25428): (KIAA1217) Predicted to be involved in embryonic skeletal system development. Predicted to be active in cytoplasm. [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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.354+13992G>A		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+13992G>A		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37657 AN: 151720 Hom.: 5449 Cov.: 32

Gnomad AFR AF: 0.0854

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.322

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.287

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

GnomAD4 genome AF: 0.248 AC: 37669 AN: 151844 Hom.: 5450 Cov.: 32 AF XY: 0.248 AC XY: 18428 AN XY: 74182

Gnomad4 AFR AF: 0.0853

Gnomad4 AMR AF: 0.293

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.355

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.307

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.287

Alfa AF: 0.278 Hom.: 839

Bravo AF: 0.238

Asia WGS AF: 0.260 AC: 905 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.0
Dann	Benign	0.57

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: rs12414014; hg19: chr10-24522830;