10-24315964-G-A

Variant names:

• chr10-24315964-G-A
• rs16924573
• NM_019590.5:c.355-64905G>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.355-64905G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0876 in 150,844 control chromosomes in the GnomAD database, including 757 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 0.088 (757 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019590.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.355-64905G>A		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-64905G>A		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.355-64905G>A		intron	N/A	NP_001269697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.355-64905G>A		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.355-64905G>A		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.355-64905G>A		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13194 AN: 150726 Hom.: 753 Cov.: 31

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.00549

Gnomad AMR AF: 0.0785

Gnomad ASJ AF: 0.0999

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.0277

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0535

Gnomad OTH AF: 0.0849

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

GnomAD4 genome AF: 0.0876 AC: 13219 AN: 150844 Hom.: 757 Cov.: 31 AF XY: 0.0869 AC XY: 6395 AN XY: 73630

African (AFR) AF: 0.150 AC: 6133 AN: 40898

American (AMR) AF: 0.0782 AC: 1184 AN: 15132

Ashkenazi Jewish (ASJ) AF: 0.0999 AC: 346 AN: 3464

East Asian (EAS) AF: 0.197 AC: 984 AN: 5006

South Asian (SAS) AF: 0.0951 AC: 452 AN: 4754

European-Finnish (FIN) AF: 0.0277 AC: 289 AN: 10440

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0535 AC: 3629 AN: 67852

Other (OTH) AF: 0.0855 AC: 179 AN: 2094

Alfa AF: 0.0647 Hom.: 428

Bravo AF: 0.0964

Asia WGS AF: 0.139 AC: 484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.027
DANN	Benign	0.40
PhyloP100		-2.1
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: rs16924573; hg19: chr10-24604893;