rs7902724

Positions:

• chr10-24382436-A-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.553+1369A>C		intron_variant		ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.553+1369A>C		intron_variant		1	NM_019590.5	ENSP00000365637	A2

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.230

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.307

Alfa AF: 0.281 Hom.: 5781

Bravo AF: 0.357

Asia WGS AF: 0.228 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.21

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

Publications

LitVar

Other links and lift over

dbSNP: rs7902724; hg19: chr10-24671365;