10-24425406-T-A

Variant names:

• chr10-24425406-T-A
• rs12411459
• NM_019590.5:c.554-7589T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019590.5(KIAA1217):​c.554-7589T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.085 in 152,242 control chromosomes in the GnomAD database, including 574 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 0.085 (574 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 0 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-7589T>A		intron_variant	Intron 3 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-7589T>A		intron_variant	Intron 3 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12923 AN: 152124 Hom.: 573 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.0424

Gnomad EAS AF: 0.0738

Gnomad SAS AF: 0.0302

Gnomad FIN AF: 0.0797

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0850 AC: 12946 AN: 152242 Hom.: 574 Cov.: 32 AF XY: 0.0832 AC XY: 6190 AN XY: 74442

African (AFR) AF: 0.113 AC: 4693 AN: 41536

American (AMR) AF: 0.0893 AC: 1367 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0424 AC: 147 AN: 3466

East Asian (EAS) AF: 0.0736 AC: 381 AN: 5176

South Asian (SAS) AF: 0.0303 AC: 146 AN: 4826

European-Finnish (FIN) AF: 0.0797 AC: 846 AN: 10612

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5070 AN: 68006

Other (OTH) AF: 0.0781 AC: 165 AN: 2114

Alfa AF: 0.0785 Hom.: 51

Bravo AF: 0.0882

Asia WGS AF: 0.0610 AC: 210 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.8
DANN	Benign	0.57
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12411459; hg19: chr10-24714335;