rs10082549

chr10-24300259-A-G

Variant summary

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

The NM_019590.5(KIAA1217):c.354+80350A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,230 control chromosomes in the GnomAD database, including 1,577 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 0.12 (1577 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.354+80350A>G		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+80350A>G		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17536 AN: 152112 Hom.: 1563 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0580

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.116 AC: 17591 AN: 152230 Hom.: 1577 Cov.: 32 AF XY: 0.115 AC XY: 8554 AN XY: 74432

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.0666

Gnomad4 ASJ AF: 0.0634

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0280

Gnomad4 NFE AF: 0.0580

Gnomad4 OTH AF: 0.120

Alfa AF: 0.108 Hom.: 205

Bravo AF: 0.124

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.55
Dann	Benign	0.67

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: rs10082549; hg19: chr10-24589188;