rs11014010

Positions:

• chr10-24301142-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.355-79727C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,094 control chromosomes in the GnomAD database, including 1,251 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 0.10 (1251 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-79727C>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.355-79727C>T		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15497 AN: 151976 Hom.: 1241 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0556

Gnomad ASJ AF: 0.0317

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0509

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.102 AC: 15539 AN: 152094 Hom.: 1251 Cov.: 32 AF XY: 0.100 AC XY: 7465 AN XY: 74350

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0317

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0264

Gnomad4 NFE AF: 0.0509

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0805 Hom.: 109

Bravo AF: 0.110

Asia WGS AF: 0.149 AC: 517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.61

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: rs11014010; hg19: chr10-24590071;