10-24275902-C-T

Position:

• chr10-24275902-C-T

Variant summary

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

The NM_019590.5(KIAA1217):​c.354+55993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 428,112 control chromosomes in the GnomAD database, including 180,223 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 0.94 (67506 hom., cov: 32)
  • Exomes 𝑓: 0.90 (112717 hom.)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.403

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.967 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.354+55993C>T		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+55993C>T		intron_variant		1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.940 AC: 143025 AN: 152122 Hom.: 67472 Cov.: 32

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.953

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.925

GnomAD4 exome AF: 0.899 AC: 248130 AN: 275872 Hom.: 112717 AF XY: 0.883 AC XY: 136641 AN XY: 154666

Gnomad4 AFR exome AF: 0.974

Gnomad4 AMR exome AF: 0.941

Gnomad4 ASJ exome AF: 0.920

Gnomad4 EAS exome AF: 0.787

Gnomad4 SAS exome AF: 0.735

Gnomad4 FIN exome AF: 0.975

Gnomad4 NFE exome AF: 0.939

Gnomad4 OTH exome AF: 0.913

GnomAD4 genome AF: 0.940 AC: 143110 AN: 152240 Hom.: 67506 Cov.: 32 AF XY: 0.938 AC XY: 69788 AN XY: 74426

Gnomad4 AFR AF: 0.975

Gnomad4 AMR AF: 0.941

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.724

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.918

Alfa AF: 0.945 Hom.: 13779

Bravo AF: 0.942

Asia WGS AF: 0.756 AC: 2633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.91
DANN	Benign	0.32

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: rs10764458; hg19: chr10-24564831;