NM_019590.5:c.355-76722A>T

Variant names:

• chr10-24304147-A-T
• rs727269
• NM_019590.5:c.355-76722A>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_019590.5(KIAA1217):​c.355-76722A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000599 in 140,250 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00060 (0 hom., cov: 25)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840
• Publications: 3 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

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.355-76722A>T		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-76722A>T		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.355-76722A>T		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.355-76722A>T		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.355-76722A>T		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.355-76722A>T		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.000599 AC: 84 AN: 140224 Hom.: 0 Cov.: 25

Gnomad AFR AF: 0.000252

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000696

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000364

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00106

Gnomad OTH AF: 0.000513

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

GnomAD4 genome AF: 0.000599 AC: 84 AN: 140250 Hom.: 0 Cov.: 25 AF XY: 0.000650 AC XY: 44 AN XY: 67738

African (AFR) AF: 0.000252 AC: 9 AN: 35734

American (AMR) AF: 0.0000695 AC: 1 AN: 14386

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3424

East Asian (EAS) AF: 0.00 AC: 0 AN: 4568

South Asian (SAS) AF: 0.00 AC: 0 AN: 4506

European-Finnish (FIN) AF: 0.000364 AC: 3 AN: 8246

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 280

European-Non Finnish (NFE) AF: 0.00106 AC: 70 AN: 66240

Other (OTH) AF: 0.000510 AC: 1 AN: 1962

Alfa AF: 0.00 Hom.: 6261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.34
PhyloP100		-0.84

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: rs727269; hg19: chr10-24593076;