rs12221235

chr10-24503786-C-G

Variant summary

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

The NM_019590.5(KIAA1217):c.2001+2241C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,246 control chromosomes in the GnomAD database, including 1,050 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 0.10 (1050 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.35

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.129 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.2001+2241C>G		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2001+2241C>G		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15142 AN: 152128 Hom.: 1042 Cov.: 33

Gnomad AFR AF: 0.0244

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0996 AC: 15159 AN: 152246 Hom.: 1050 Cov.: 33 AF XY: 0.104 AC XY: 7736 AN XY: 74440

Gnomad4 AFR AF: 0.0244

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0510

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0862

Alfa AF: 0.112 Hom.: 138

Bravo AF: 0.0894

Asia WGS AF: 0.0810 AC: 283 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.041
Dann	Benign	0.44

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: rs12221235; hg19: chr10-24792715;