10-24284050-T-C

Position:

• chr10-24284050-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+64141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,552 control chromosomes in the GnomAD database, including 19,925 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 0.50 (19925 hom., cov: 29)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.586 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.354+64141T>C		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+64141T>C		intron_variant		1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76018 AN: 151436 Hom.: 19924 Cov.: 29

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.581

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.502 AC: 76050 AN: 151552 Hom.: 19925 Cov.: 29 AF XY: 0.497 AC XY: 36821 AN XY: 74076

Gnomad4 AFR AF: 0.592

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.257

Gnomad4 FIN AF: 0.581

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.466

Alfa AF: 0.404 Hom.: 1173

Bravo AF: 0.497

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs220361; hg19: chr10-24572979; COSMIC: COSV64601871;