10-24338709-A-T

Variant names:

• chr10-24338709-A-T
• rs428364
• NM_019590.5:c.355-42160A>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.355-42160A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 152,070 control chromosomes in the GnomAD database, including 29,601 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 0.60 (29601 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.355-42160A>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.355-42160A>T		intron_variant	Intron 2 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91291 AN: 151952 Hom.: 29551 Cov.: 33

Gnomad AFR AF: 0.852

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.601 AC: 91400 AN: 152070 Hom.: 29601 Cov.: 33 AF XY: 0.603 AC XY: 44844 AN XY: 74320

African (AFR) AF: 0.852 AC: 35371 AN: 41512

American (AMR) AF: 0.468 AC: 7159 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1553 AN: 3470

East Asian (EAS) AF: 0.784 AC: 4049 AN: 5166

South Asian (SAS) AF: 0.638 AC: 3077 AN: 4822

European-Finnish (FIN) AF: 0.555 AC: 5852 AN: 10538

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32599 AN: 67958

Other (OTH) AF: 0.563 AC: 1192 AN: 2116

Alfa AF: 0.540 Hom.: 2804

Bravo AF: 0.606

Asia WGS AF: 0.722 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.3
DANN	Benign	0.76
PhyloP100		-0.36
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: rs428364; hg19: chr10-24627638;