rs3762085

chr10-24431515-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.554-1480C>T		intron_variant		ENST00000376454.8
LOC124902395	XR_007062090.1	n.191G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-1480C>T		intron_variant		1	NM_019590.5	A2

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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.359

Gnomad4 OTH AF: 0.354

Alfa AF: 0.357 Hom.: 13523

Bravo AF: 0.399

Asia WGS AF: 0.315 AC: 1094 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.32

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

Publications

LitVar

Other links and lift over

dbSNP: rs3762085; hg19: chr10-24720444;