rs16924404

chr10-24231719-G-Achr10-24231719-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+11810G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 151,456 control chromosomes in the GnomAD database, including 3,908 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 0.23 (3908 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.179

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.354+11810G>A		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+11810G>A		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34139 AN: 151366 Hom.: 3909 Cov.: 31

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.225 AC: 34153 AN: 151456 Hom.: 3908 Cov.: 31 AF XY: 0.225 AC XY: 16655 AN XY: 73960

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.211

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.254

Alfa AF: 0.184 Hom.: 686

Bravo AF: 0.220

Asia WGS AF: 0.286 AC: 996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.2
Dann	Benign	0.58

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: rs16924404; hg19: chr10-24520648;