chr10-23941311-C-T

Variant names:

• chr10-23941311-C-T
• rs11013804
• ENST00000376462.5:c.-320-65914C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.91).
• 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 rank	MANE	Protein	UniProt
KIAA1217	NM_001098500.3	c.-320-65914C>T		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.-320-65914C>T		intron_variant	Intron 1 of 18	1		ENSP00000365645.1

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

African (AFR) AF: 0.142 AC: 5915 AN: 41512

American (AMR) AF: 0.204 AC: 3116 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1039 AN: 3470

East Asian (EAS) AF: 0.0773 AC: 400 AN: 5172

South Asian (SAS) AF: 0.203 AC: 979 AN: 4816

European-Finnish (FIN) AF: 0.202 AC: 2132 AN: 10540

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.239 AC: 16256 AN: 67978

Other (OTH) AF: 0.208 AC: 439 AN: 2108

Alfa AF: 0.239 Hom.: 4974

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
PhyloP100		-0.015
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: rs11013804; hg19: chr10-24230240;