rs11013962

Positions:

• chr10-24206657-A-G
• chr10-24206657-A-T

Variant summary

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

The NM_001098500.3(KIAA1217):​c.-170-12969A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,076 control chromosomes in the GnomAD database, including 18,483 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 0.49 (18483 hom., cov: 33)
• Consequence: KIAA1217 NM_001098500.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

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=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_001098500.3	c.-170-12969A>G		intron_variant			NP_001091970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376462.5	c.-170-12969A>G		intron_variant		1		ENSP00000365645.1
KIAA1217	ENST00000636305.1	c.212-12969A>G		intron_variant		5		ENSP00000489926.1

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74104 AN: 151958 Hom.: 18480 Cov.: 33

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.488 AC: 74145 AN: 152076 Hom.: 18483 Cov.: 33 AF XY: 0.488 AC XY: 36249 AN XY: 74326

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.651

Gnomad4 SAS AF: 0.573

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.546

Alfa AF: 0.532 Hom.: 39167

Bravo AF: 0.480

Asia WGS AF: 0.615 AC: 2137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	9.1
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11013962; hg19: chr10-24495586;