rs7904115

chr10-24504238-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.2001+2693C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 152,124 control chromosomes in the GnomAD database, including 7,231 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 0.30 (7231 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIAA1217	NM_019590.5	c.2001+2693C>T		intron_variant		ENST00000376454.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2001+2693C>T		intron_variant		1	NM_019590.5	A2

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45879 AN: 152006 Hom.: 7227 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.302 AC: 45895 AN: 152124 Hom.: 7231 Cov.: 33 AF XY: 0.299 AC XY: 22261 AN XY: 74352

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.304

Alfa AF: 0.294 Hom.: 833

Bravo AF: 0.308

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
Cadd	Benign	9.9
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7904115; hg19: chr10-24793167;