10-24347012-T-C

Variant names:

• chr10-24347012-T-C
• rs7091189
• NM_019590.5:c.355-33857T>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.355-33857T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,080 control chromosomes in the GnomAD database, including 35,168 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 0.68 (35168 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-33857T>C		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.355-33857T>C		intron_variant	Intron 2 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102897 AN: 151962 Hom.: 35134 Cov.: 32

Gnomad AFR AF: 0.663

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.677 AC: 102979 AN: 152080 Hom.: 35168 Cov.: 32 AF XY: 0.681 AC XY: 50605 AN XY: 74322

African (AFR) AF: 0.663 AC: 27487 AN: 41462

American (AMR) AF: 0.533 AC: 8141 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2364 AN: 3466

East Asian (EAS) AF: 0.820 AC: 4245 AN: 5176

South Asian (SAS) AF: 0.790 AC: 3808 AN: 4820

European-Finnish (FIN) AF: 0.757 AC: 8000 AN: 10566

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46627 AN: 67998

Other (OTH) AF: 0.674 AC: 1422 AN: 2110

Alfa AF: 0.657 Hom.: 5634

Bravo AF: 0.654

Asia WGS AF: 0.777 AC: 2702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.42
PhyloP100		-0.18
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: rs7091189; hg19: chr10-24635941;