rs2297330

chr10-24521734-C-Achr10-24521734-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.2309-48C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,586,438 control chromosomes in the GnomAD database, including 33,189 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 0.20 (3226 hom., cov: 31)
  • Exomes 𝑓: 0.20 (29963 hom.)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23

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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.2309-48C>A		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2309-48C>A		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30555 AN: 151918 Hom.: 3225 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.209

GnomAD3 exomes AF: 0.194 AC: 45525 AN: 235070 Hom.: 4538 AF XY: 0.193 AC XY: 24561 AN XY: 127274

Gnomad AFR exome AF: 0.201

Gnomad AMR exome AF: 0.192

Gnomad ASJ exome AF: 0.221

Gnomad EAS exome AF: 0.0951

Gnomad SAS exome AF: 0.145

Gnomad FIN exome AF: 0.190

Gnomad NFE exome AF: 0.220

Gnomad OTH exome AF: 0.211

GnomAD4 exome AF: 0.202 AC: 289795 AN: 1434402 Hom.: 29963 Cov.: 30 AF XY: 0.200 AC XY: 142564 AN XY: 711318

Gnomad4 AFR exome AF: 0.210

Gnomad4 AMR exome AF: 0.195

Gnomad4 ASJ exome AF: 0.222

Gnomad4 EAS exome AF: 0.101

Gnomad4 SAS exome AF: 0.148

Gnomad4 FIN exome AF: 0.196

Gnomad4 NFE exome AF: 0.209

Gnomad4 OTH exome AF: 0.203

GnomAD4 genome AF: 0.201 AC: 30554 AN: 152036 Hom.: 3226 Cov.: 31 AF XY: 0.199 AC XY: 14817 AN XY: 74300

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.206

Alfa AF: 0.213 Hom.: 5079

Bravo AF: 0.203

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	0.0050
Dann	Benign	0.63

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: rs2297330; hg19: chr10-24810663; COSMIC: COSV56824489;