rs12221235

Variant names:

• chr10-24503786-C-G
• rs12221235
• NM_019590.5:c.2001+2241C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.2001+2241C>G		intron_variant	Intron 9 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2001+2241C>G		intron_variant	Intron 9 of 20	1	NM_019590.5	ENSP00000365637.3

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

African (AFR) AF: 0.0244 AC: 1013 AN: 41566

American (AMR) AF: 0.118 AC: 1809 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3472

East Asian (EAS) AF: 0.138 AC: 713 AN: 5176

South Asian (SAS) AF: 0.0315 AC: 152 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2607 AN: 10582

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8311 AN: 68014

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

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
PhyloP100		-3.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12221235; hg19: chr10-24792715;