rs10828564

Variant names:

• chr10-23885258-T-C
• rs10828564
• ENST00000376462.5:c.-320-121967T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000376462.5(KIAA1217):​c.-320-121967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 151,732 control chromosomes in the GnomAD database, including 3,039 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 (3039 hom., cov: 32)
• Consequence: KIAA1217 ENST00000376462.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_001098500.3	c.-320-121967T>C		intron_variant	Intron 1 of 18		NP_001091970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376462.5	c.-320-121967T>C		intron_variant	Intron 1 of 18	1		ENSP00000365645.1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29803 AN: 151612 Hom.: 3042 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.197 AC: 29824 AN: 151732 Hom.: 3039 Cov.: 32 AF XY: 0.194 AC XY: 14408 AN XY: 74114

African (AFR) AF: 0.217 AC: 8969 AN: 41402

American (AMR) AF: 0.186 AC: 2837 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 920 AN: 3462

East Asian (EAS) AF: 0.192 AC: 982 AN: 5110

South Asian (SAS) AF: 0.131 AC: 628 AN: 4812

European-Finnish (FIN) AF: 0.213 AC: 2254 AN: 10568

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12572 AN: 67846

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.190 Hom.: 1883

Bravo AF: 0.196

Asia WGS AF: 0.144 AC: 499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.65
PhyloP100		-0.19
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10828564; hg19: chr10-24174187;