rs7078849

Positions:

• chr10-24517583-T-C

Variant summary

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

The ENST00000376454.8(KIAA1217):​c.2178-2540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,108 control chromosomes in the GnomAD database, including 7,349 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 (7349 hom., cov: 33)
• Consequence: KIAA1217 ENST00000376454.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.2178-2540T>C		intron_variant		ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2178-2540T>C		intron_variant		1	NM_019590.5	ENSP00000365637	A2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46120 AN: 151990 Hom.: 7346 Cov.: 33

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.303 AC: 46132 AN: 152108 Hom.: 7349 Cov.: 33 AF XY: 0.301 AC XY: 22355 AN XY: 74360

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.292

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.306

Alfa AF: 0.295 Hom.: 841

Bravo AF: 0.310

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.83
DANN	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99

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: rs7078849; hg19: chr10-24806512;