rs2428307

Positions:

• chr10-24358635-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019590.5(KIAA1217):​c.355-22234T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,186 control chromosomes in the GnomAD database, including 18,620 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 0.48 (18620 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

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 = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-22234T>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.355-22234T>C		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72735 AN: 152068 Hom.: 18585 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.521

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.479 AC: 72823 AN: 152186 Hom.: 18620 Cov.: 33 AF XY: 0.475 AC XY: 35331 AN XY: 74406

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.301

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.494

Alfa AF: 0.423 Hom.: 7101

Bravo AF: 0.499

Asia WGS AF: 0.557 AC: 1936 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	2.4
DANN	Benign	0.52

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: rs2428307; hg19: chr10-24647564;