chr10-24308053-A-T

Variant names:

• chr10-24308053-A-T
• rs7917252
• NM_019590.5:c.355-72816A>T

Variant summary

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

The NM_019590.5(KIAA1217):​c.355-72816A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0917 in 152,254 control chromosomes in the GnomAD database, including 1,022 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 0.092 (1022 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-72816A>T		intron_variant	Intron 2 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.355-72816A>T		intron_variant	Intron 2 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13922 AN: 152136 Hom.: 1014 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0482

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0971

Gnomad FIN AF: 0.0244

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0446

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0917 AC: 13962 AN: 152254 Hom.: 1022 Cov.: 32 AF XY: 0.0899 AC XY: 6689 AN XY: 74438

African (AFR) AF: 0.201 AC: 8362 AN: 41536

American (AMR) AF: 0.0482 AC: 738 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3470

East Asian (EAS) AF: 0.151 AC: 783 AN: 5182

South Asian (SAS) AF: 0.0976 AC: 471 AN: 4826

European-Finnish (FIN) AF: 0.0244 AC: 259 AN: 10600

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0445 AC: 3029 AN: 68022

Other (OTH) AF: 0.0908 AC: 192 AN: 2114

Alfa AF: 0.0733 Hom.: 86

Bravo AF: 0.0989

Asia WGS AF: 0.110 AC: 383 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		0.11
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: rs7917252; hg19: chr10-24596982;