rs3818672

chr10-24494464-C-Achr10-24494464-C-G

Variant summary

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

The NM_019590.5(KIAA1217):c.1680-36C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,553,722 control chromosomes in the GnomAD database, including 38,737 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 0.25 (5381 hom., cov: 32)
  • Exomes 𝑓: 0.21 (33356 hom.)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.44

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=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.1680-36C>A		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.1680-36C>A		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37760 AN: 151658 Hom.: 5364 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.264

GnomAD3 exomes AF: 0.238 AC: 59307 AN: 249068 Hom.: 7795 AF XY: 0.240 AC XY: 32369 AN XY: 134708

Gnomad AFR exome AF: 0.365

Gnomad AMR exome AF: 0.243

Gnomad ASJ exome AF: 0.208

Gnomad EAS exome AF: 0.355

Gnomad SAS exome AF: 0.373

Gnomad FIN exome AF: 0.129

Gnomad NFE exome AF: 0.187

Gnomad OTH exome AF: 0.231

GnomAD4 exome AF: 0.208 AC: 291256 AN: 1401944 Hom.: 33356 Cov.: 22 AF XY: 0.212 AC XY: 148977 AN XY: 701138

Gnomad4 AFR exome AF: 0.371

Gnomad4 AMR exome AF: 0.241

Gnomad4 ASJ exome AF: 0.203

Gnomad4 EAS exome AF: 0.358

Gnomad4 SAS exome AF: 0.370

Gnomad4 FIN exome AF: 0.135

Gnomad4 NFE exome AF: 0.185

Gnomad4 OTH exome AF: 0.234

GnomAD4 genome AF: 0.249 AC: 37817 AN: 151778 Hom.: 5381 Cov.: 32 AF XY: 0.247 AC XY: 18358 AN XY: 74198

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.270

Alfa AF: 0.221 Hom.: 915

Bravo AF: 0.264

Asia WGS AF: 0.388 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	14
Dann	Benign	0.61

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: rs3818672; hg19: chr10-24783393; COSMIC: COSV56817428; COSMIC: COSV56817428;