chr10-24517583-T-C

Variant names:

• chr10-24517583-T-C
• rs7078849
• NM_019590.5:c.2178-2540T>C

Variant summary

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

The NM_019590.5(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 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• 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=-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 rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.2178-2540T>C		intron_variant	Intron 10 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.2178-2540T>C		intron_variant	Intron 10 of 20	1	NM_019590.5	ENSP00000365637.3

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

African (AFR) AF: 0.393 AC: 16296 AN: 41476

American (AMR) AF: 0.268 AC: 4094 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 1012 AN: 3470

East Asian (EAS) AF: 0.153 AC: 794 AN: 5174

South Asian (SAS) AF: 0.267 AC: 1287 AN: 4818

European-Finnish (FIN) AF: 0.267 AC: 2824 AN: 10584

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.275 AC: 18711 AN: 67992

Other (OTH) AF: 0.306 AC: 646 AN: 2108

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
PhyloP100		-1.8
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99
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: rs7078849; hg19: chr10-24806512;