rs1336188

chr10-24274061-T-C

Variant summary

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

The NM_019590.5(KIAA1217):c.354+54152T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 152,056 control chromosomes in the GnomAD database, including 8,459 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 0.31 (8459 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0890

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.354+54152T>C		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+54152T>C		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46588 AN: 151938 Hom.: 8463 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.464

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.306 AC: 46595 AN: 152056 Hom.: 8459 Cov.: 32 AF XY: 0.309 AC XY: 22942 AN XY: 74326

Gnomad4 AFR AF: 0.114

Gnomad4 AMR AF: 0.464

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.331

Alfa AF: 0.355 Hom.: 5109

Bravo AF: 0.302

Asia WGS AF: 0.257 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.0
Dann	Benign	0.34

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: rs1336188; hg19: chr10-24562990;