rs1335826

Positions:

• chr10-23755536-T-C
• chr10-23755536-T-G

Variant summary

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

The ENST00000376462.5(KIAA1217):​c.-321+60302T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,112 control chromosomes in the GnomAD database, including 19,046 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 0.43 (19046 hom., cov: 32)
• Consequence: KIAA1217 ENST00000376462.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_001098500.3	c.-321+60302T>C		intron_variant			NP_001091970.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376462.5	c.-321+60302T>C		intron_variant		1		ENSP00000365645	A2
KIAA1217	ENST00000481700.1	n.453+60302T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65341 AN: 151992 Hom.: 18991 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.430 AC: 65452 AN: 152112 Hom.: 19046 Cov.: 32 AF XY: 0.428 AC XY: 31801 AN XY: 74370

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.399

Alfa AF: 0.261 Hom.: 2610

Bravo AF: 0.459

Asia WGS AF: 0.303 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.8
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335826; hg19: chr10-24044465;