rs12412510

chr10-24409406-A-Cchr10-24409406-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019590.5(KIAA1217):c.554-23589A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0536 in 152,210 control chromosomes in the GnomAD database, including 219 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 0.054 (219 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0679 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.554-23589A>C		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-23589A>C		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8157 AN: 152092 Hom.: 219 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0574

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0536 AC: 8160 AN: 152210 Hom.: 219 Cov.: 32 AF XY: 0.0523 AC XY: 3889 AN XY: 74424

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.0714

Gnomad4 ASJ AF: 0.0323

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.0417

Gnomad4 FIN AF: 0.0370

Gnomad4 NFE AF: 0.0574

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0138 Hom.: 5

Bravo AF: 0.0568

Asia WGS AF: 0.0560 AC: 194 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	0.40
Dann	Benign	0.57

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: rs12412510; hg19: chr10-24698335;