rs2285592

Variant names:

• chr10-24316966-T-C
• rs2285592
• NM_019590.5:c.355-63903T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019590.5(KIAA1217):​c.355-63903T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,070 control chromosomes in the GnomAD database, including 1,713 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 0.12 (1713 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-63903T>C		intron_variant	Intron 2 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.355-63903T>C		intron_variant	Intron 2 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18016 AN: 151952 Hom.: 1706 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0899

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.119 AC: 18050 AN: 152070 Hom.: 1713 Cov.: 32 AF XY: 0.117 AC XY: 8685 AN XY: 74356

African (AFR) AF: 0.256 AC: 10606 AN: 41452

American (AMR) AF: 0.0896 AC: 1368 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.193 AC: 996 AN: 5154

South Asian (SAS) AF: 0.0968 AC: 466 AN: 4814

European-Finnish (FIN) AF: 0.0304 AC: 322 AN: 10604

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3690 AN: 67990

Other (OTH) AF: 0.107 AC: 225 AN: 2112

Alfa AF: 0.0995 Hom.: 181

Bravo AF: 0.129

Asia WGS AF: 0.141 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	15
DANN	Benign	0.74
PhyloP100		0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2285592; hg19: chr10-24605895;