chr10-24257812-G-A

Position:

• chr10-24257812-G-A

Variant summary

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

The NM_019590.5(KIAA1217):​c.354+37903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 151,902 control chromosomes in the GnomAD database, including 6,324 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 0.27 (6324 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275

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 (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.354+37903G>A		intron_variant		ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+37903G>A		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41334 AN: 151788 Hom.: 6328 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.272 AC: 41339 AN: 151902 Hom.: 6324 Cov.: 31 AF XY: 0.271 AC XY: 20074 AN XY: 74202

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.295

Alfa AF: 0.333 Hom.: 11467

Bravo AF: 0.261

Asia WGS AF: 0.230 AC: 803 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	1.3
DANN	Benign	0.48

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: rs12782581; hg19: chr10-24546741; COSMIC: COSV64613799; COSMIC: COSV64613799;