10-24544776-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_019590.5(KIAA1217):c.5212-205A>G variant causes a intron change. The variant allele was found at a frequency of 0.0753 in 152,170 control chromosomes in the GnomAD database, including 648 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 0.075 (648 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.06

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.5212-205A>G		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.5212-205A>G		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11443 AN: 152052 Hom.: 640 Cov.: 32

Gnomad AFR AF: 0.0372

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0753 AC: 11459 AN: 152170 Hom.: 648 Cov.: 32 AF XY: 0.0817 AC XY: 6079 AN XY: 74386

Gnomad4 AFR AF: 0.0373

Gnomad4 AMR AF: 0.140

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.0611 Hom.: 566

Bravo AF: 0.0772

Asia WGS AF: 0.238 AC: 824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
Cadd	Benign	17
Dann	Benign	0.76

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: rs1888656; hg19: chr10-24833705;