rs16924809

Positions:

• chr10-24470725-C-T

Variant summary

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

The NM_019590.5(KIAA1217):​c.847-2503C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 152,188 control chromosomes in the GnomAD database, including 710 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 0.079 (710 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.847-2503C>T		intron_variant		ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.847-2503C>T		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11973 AN: 152070 Hom.: 703 Cov.: 32

Gnomad AFR AF: 0.0169

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0476

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0328

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0890

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0788 AC: 11988 AN: 152188 Hom.: 710 Cov.: 32 AF XY: 0.0852 AC XY: 6337 AN XY: 74388

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0476

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.0610

Alfa AF: 0.0791 Hom.: 111

Bravo AF: 0.0683

Asia WGS AF: 0.0780 AC: 271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.016
DANN	Benign	0.37

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: rs16924809; hg19: chr10-24759654;