rs7096689

Variant names:

• chr10-24408931-A-G
• rs7096689
• NM_019590.5:c.554-24064A>G

Variant summary

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

The NM_019590.5(KIAA1217):​c.554-24064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0916 in 152,276 control chromosomes in the GnomAD database, including 1,454 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 (1454 hom., cov: 33)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 1 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 = 0.248 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-24064A>G		intron_variant	Intron 3 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-24064A>G		intron_variant	Intron 3 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13920 AN: 152158 Hom.: 1451 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0527

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.00786

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0264

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0916 AC: 13946 AN: 152276 Hom.: 1454 Cov.: 33 AF XY: 0.0889 AC XY: 6618 AN XY: 74462

African (AFR) AF: 0.252 AC: 10475 AN: 41524

American (AMR) AF: 0.0540 AC: 827 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3466

East Asian (EAS) AF: 0.0526 AC: 273 AN: 5186

South Asian (SAS) AF: 0.00766 AC: 37 AN: 4828

European-Finnish (FIN) AF: 0.0122 AC: 130 AN: 10622

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0264 AC: 1795 AN: 68028

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0444 Hom.: 994

Bravo AF: 0.104

Asia WGS AF: 0.0360 AC: 126 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	5.5
DANN	Benign	0.52
PhyloP100		0.31
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: rs7096689; hg19: chr10-24697860;