NM_019590.5:c.355-77034G>A

Variant names:

• chr10-24303835-G-A
• rs220366
• NM_019590.5:c.355-77034G>A

Variant summary

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

The NM_019590.5(KIAA1217):​c.355-77034G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.777 in 152,036 control chromosomes in the GnomAD database, including 47,859 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 0.78 (47859 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019590.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	NM_019590.5	MANE Select	c.355-77034G>A		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-77034G>A		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.355-77034G>A		intron	N/A	NP_001269697.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIAA1217	ENST00000376454.8	TSL:1 MANE Select	c.355-77034G>A		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.355-77034G>A		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.355-77034G>A		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118059 AN: 151918 Hom.: 47861 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.777 AC: 118074 AN: 152036 Hom.: 47859 Cov.: 31 AF XY: 0.777 AC XY: 57758 AN XY: 74352

African (AFR) AF: 0.564 AC: 23362 AN: 41406

American (AMR) AF: 0.858 AC: 13094 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2931 AN: 3472

East Asian (EAS) AF: 0.457 AC: 2356 AN: 5150

South Asian (SAS) AF: 0.565 AC: 2722 AN: 4820

European-Finnish (FIN) AF: 0.956 AC: 10131 AN: 10594

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60842 AN: 68014

Other (OTH) AF: 0.765 AC: 1616 AN: 2112

Alfa AF: 0.852 Hom.: 101694

Bravo AF: 0.761

Asia WGS AF: 0.549 AC: 1914 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.066
DANN	Benign	0.62
PhyloP100		-0.69
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: rs220366; hg19: chr10-24592764;