chr10-24256130-A-T

Position:

• chr10-24256130-A-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+36221A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 150,686 control chromosomes in the GnomAD database, including 39,998 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 0.73 (39998 hom., cov: 27)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.354+36221A>T		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.354+36221A>T		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.727 AC: 109427 AN: 150576 Hom.: 39973 Cov.: 27

Gnomad AFR AF: 0.704

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.727 AC: 109498 AN: 150686 Hom.: 39998 Cov.: 27 AF XY: 0.726 AC XY: 53290 AN XY: 73438

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.612

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.711

Alfa AF: 0.749 Hom.: 5321

Bravo AF: 0.729

Asia WGS AF: 0.608 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.70
DANN	Benign	0.80

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: rs2280172; hg19: chr10-24545059;