rs11013804

chr10-23941311-C-T

Variant summary

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

The ENST00000376462.5(KIAA1217):c.-320-65914C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,076 control chromosomes in the GnomAD database, including 3,320 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 0.20 (3320 hom., cov: 32)
• Consequence: KIAA1217 ENST00000376462.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_001098500.3	c.-320-65914C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376462.5	c.-320-65914C>T		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30466 AN: 151958 Hom.: 3319 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0770

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.280

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.200 AC: 30482 AN: 152076 Hom.: 3320 Cov.: 32 AF XY: 0.200 AC XY: 14859 AN XY: 74324

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0773

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.208

Alfa AF: 0.242 Hom.: 4263

Bravo AF: 0.199

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11013804; hg19: chr10-24230240;