10-24382044-T-C

Position:

• chr10-24382044-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.553+977T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 150,770 control chromosomes in the GnomAD database, including 11,311 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 0.38 (11311 hom., cov: 28)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.553+977T>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.553+977T>C		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 57823 AN: 150670 Hom.: 11284 Cov.: 28

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.384 AC: 57905 AN: 150770 Hom.: 11311 Cov.: 28 AF XY: 0.386 AC XY: 28383 AN XY: 73624

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.398

Alfa AF: 0.386 Hom.: 18765

Bravo AF: 0.384

Asia WGS AF: 0.488 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.8
DANN	Benign	0.53

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: rs7081094; hg19: chr10-24670973;