chr10-24416906-C-G

Variant names:

• chr10-24416906-C-G
• rs3847376
• NM_019590.5:c.554-16089C>G

Variant summary

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

The NM_019590.5(KIAA1217):​c.554-16089C>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
• Publications: 0 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-16089C>G		intron_variant	Intron 3 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-16089C>G		intron_variant	Intron 3 of 20	1	NM_019590.5	ENSP00000365637.3

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

African (AFR) AF: 0.582 AC: 24095 AN: 41376

American (AMR) AF: 0.291 AC: 4440 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 741 AN: 3466

East Asian (EAS) AF: 0.275 AC: 1410 AN: 5134

South Asian (SAS) AF: 0.213 AC: 1023 AN: 4808

European-Finnish (FIN) AF: 0.332 AC: 3506 AN: 10550

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18145 AN: 67932

Other (OTH) AF: 0.334 AC: 704 AN: 2106

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
PhyloP100		-0.70
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: rs3847376; hg19: chr10-24705835;