chr10-24304147-A-C

Position:

• chr10-24304147-A-C

Variant summary

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

The NM_019590.5(KIAA1217):​c.355-76722A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 140,068 control chromosomes in the GnomAD database, including 12,362 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 0.40 (12362 hom., cov: 25)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.355-76722A>C		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.355-76722A>C		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.397 AC: 55595 AN: 140042 Hom.: 12365 Cov.: 25

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.397 AC: 55570 AN: 140068 Hom.: 12362 Cov.: 25 AF XY: 0.400 AC XY: 27055 AN XY: 67612

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.436

Alfa AF: 0.409 Hom.: 5445

Bravo AF: 0.376

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.47

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: rs727269; hg19: chr10-24593076;