10-24435406-A-G

Variant names:

• chr10-24435406-A-G
• rs16924760
• NM_019590.5:c.752+2213A>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.752+2213A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,230 control chromosomes in the GnomAD database, including 6,254 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 0.27 (6254 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.462
• 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]

LOC124902395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.752+2213A>G		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.752+2213A>G		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.752+2213A>G		intron	N/A	NP_001269697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.752+2213A>G		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.752+2213A>G		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.752+2213A>G		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41720 AN: 152112 Hom.: 6233 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.275 AC: 41789 AN: 152230 Hom.: 6254 Cov.: 33 AF XY: 0.276 AC XY: 20567 AN XY: 74434

African (AFR) AF: 0.407 AC: 16896 AN: 41530

American (AMR) AF: 0.236 AC: 3611 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 775 AN: 3468

East Asian (EAS) AF: 0.200 AC: 1036 AN: 5182

South Asian (SAS) AF: 0.195 AC: 941 AN: 4832

European-Finnish (FIN) AF: 0.308 AC: 3261 AN: 10598

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14430 AN: 68012

Other (OTH) AF: 0.242 AC: 510 AN: 2110

Alfa AF: 0.233 Hom.: 18979

Bravo AF: 0.277

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.69
PhyloP100		0.46
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: rs16924760; hg19: chr10-24724335;