NM_019590.5:c.554-1480C>T

Variant names:

• chr10-24431515-C-T
• rs3762085
• NM_019590.5:c.554-1480C>T

Variant summary

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

The NM_019590.5(KIAA1217):​c.554-1480C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,876 control chromosomes in the GnomAD database, including 12,585 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 0.40 (12585 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 2 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]

LOC124902395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 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.554-1480C>T		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.554-1480C>T		intron	N/A	NP_001269696.1	Q5T5P2-10
	KIAA1217	NM_001282768.2		c.554-1480C>T		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.554-1480C>T		intron	N/A	ENSP00000365637.3	Q5T5P2-1
	KIAA1217	ENST00000376452.7	TSL:1	c.554-1480C>T		intron	N/A	ENSP00000365635.3	Q5T5P2-10
	KIAA1217	ENST00000458595.5	TSL:1	c.554-1480C>T		intron	N/A	ENSP00000392625.1	Q5T5P2-7

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60924 AN: 151760 Hom.: 12563 Cov.: 31

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.402 AC: 60993 AN: 151876 Hom.: 12585 Cov.: 31 AF XY: 0.404 AC XY: 29960 AN XY: 74232

African (AFR) AF: 0.508 AC: 21026 AN: 41380

American (AMR) AF: 0.336 AC: 5123 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1012 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1896 AN: 5166

South Asian (SAS) AF: 0.298 AC: 1432 AN: 4806

European-Finnish (FIN) AF: 0.469 AC: 4943 AN: 10536

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24359 AN: 67942

Other (OTH) AF: 0.354 AC: 746 AN: 2108

Alfa AF: 0.362 Hom.: 17443

Bravo AF: 0.399

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.32
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: rs3762085; hg19: chr10-24720444;