rs3847376

Positions:

• chr10-24416906-C-G
• chr10-24416906-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.554-16089C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,844 control chromosomes in the GnomAD database, including 11,296 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 0.36 (11296 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.554-16089C>G		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-16089C>G		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54308 AN: 151728 Hom.: 11256 Cov.: 31

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.358 AC: 54407 AN: 151844 Hom.: 11296 Cov.: 31 AF XY: 0.355 AC XY: 26326 AN XY: 74216

Gnomad4 AFR AF: 0.582

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.267

Gnomad4 OTH AF: 0.334

Alfa AF: 0.149 Hom.: 246

Bravo AF: 0.370

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.20

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: rs3847376; hg19: chr10-24705835;