rs7902724

Variant names:

• chr10-24382436-A-C
• rs7902724
• NM_019590.5:c.553+1369A>C

Variant summary

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

The NM_019590.5(KIAA1217):​c.553+1369A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,894 control chromosomes in the GnomAD database, including 10,661 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 0.35 (10661 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• 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 -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 = 0.57 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.553+1369A>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.553+1369A>C		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.553+1369A>C		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.553+1369A>C		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.553+1369A>C		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.553+1369A>C		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52742 AN: 151776 Hom.: 10652 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.347 AC: 52767 AN: 151894 Hom.: 10661 Cov.: 31 AF XY: 0.340 AC XY: 25265 AN XY: 74202

African (AFR) AF: 0.576 AC: 23841 AN: 41416

American (AMR) AF: 0.240 AC: 3656 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1006 AN: 3468

East Asian (EAS) AF: 0.230 AC: 1185 AN: 5160

South Asian (SAS) AF: 0.197 AC: 949 AN: 4810

European-Finnish (FIN) AF: 0.255 AC: 2688 AN: 10542

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18460 AN: 67944

Other (OTH) AF: 0.307 AC: 647 AN: 2108

Alfa AF: 0.294 Hom.: 8774

Bravo AF: 0.357

Asia WGS AF: 0.228 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.21
PhyloP100		-0.31
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: rs7902724; hg19: chr10-24671365;