chr10-24346027-A-G

Variant names:

• chr10-24346027-A-G
• rs2484873
• NM_019590.5:c.355-34842A>G

Variant summary

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

The NM_019590.5(KIAA1217):​c.355-34842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.875 in 152,180 control chromosomes in the GnomAD database, including 59,037 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 0.88 (59037 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 6 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.355-34842A>G		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-34842A>G		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.355-34842A>G		intron	N/A	NP_001269697.1	Q5T5P2-7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.355-34842A>G		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.355-34842A>G		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.355-34842A>G		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133108 AN: 152062 Hom.: 59005 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.953

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.887

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.875 AC: 133194 AN: 152180 Hom.: 59037 Cov.: 32 AF XY: 0.874 AC XY: 65051 AN XY: 74404

African (AFR) AF: 0.780 AC: 32327 AN: 41468

American (AMR) AF: 0.762 AC: 11635 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.953 AC: 3308 AN: 3472

East Asian (EAS) AF: 0.696 AC: 3599 AN: 5168

South Asian (SAS) AF: 0.887 AC: 4283 AN: 4830

European-Finnish (FIN) AF: 0.976 AC: 10359 AN: 10612

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64713 AN: 68032

Other (OTH) AF: 0.888 AC: 1880 AN: 2116

Alfa AF: 0.921 Hom.: 219759

Bravo AF: 0.849

Asia WGS AF: 0.797 AC: 2774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		-0.090
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: rs2484873; hg19: chr10-24634956;