10-24492661-C-G

Variant names:

• chr10-24492661-C-G
• rs4586050
• NM_019590.5:c.1680-1839C>G

Variant summary

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

The NM_019590.5(KIAA1217):​c.1680-1839C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,898 control chromosomes in the GnomAD database, including 19,414 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 0.50 (19414 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 3 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019590.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.1680-1839C>G		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.1680-2486C>G		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.1680-2486C>G		intron	N/A	NP_001269697.1	Q5T5P2-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.1680-1839C>G		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376451.4	TSL:1	c.834-2486C>G		intron	N/A	ENSP00000365634.2	Q5T5P2-3
	KIAA1217	ENST00000376452.7	TSL:1	c.1680-2486C>G		intron	N/A	ENSP00000365635.3	Q5T5P2-10

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76149 AN: 151780 Hom.: 19380 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.502 AC: 76239 AN: 151898 Hom.: 19414 Cov.: 32 AF XY: 0.505 AC XY: 37488 AN XY: 74236

African (AFR) AF: 0.576 AC: 23861 AN: 41406

American (AMR) AF: 0.446 AC: 6812 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.382 AC: 1328 AN: 3472

East Asian (EAS) AF: 0.519 AC: 2665 AN: 5132

South Asian (SAS) AF: 0.559 AC: 2687 AN: 4804

European-Finnish (FIN) AF: 0.549 AC: 5797 AN: 10550

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31536 AN: 67936

Other (OTH) AF: 0.476 AC: 1003 AN: 2106

Alfa AF: 0.330 Hom.: 813

Bravo AF: 0.495

Asia WGS AF: 0.552 AC: 1918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-1.6
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: rs4586050; hg19: chr10-24781590;