10-24217199-G-A

Variant names:

• chr10-24217199-G-A
• rs11013977
• NM_019590.5:c.71-2427G>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.71-2427G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,994 control chromosomes in the GnomAD database, including 5,493 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 0.24 (5493 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• 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 = 0.33 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.71-2427G>A		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.71-2427G>A		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.71-2427G>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.71-2427G>A		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.71-2427G>A		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.71-2427G>A		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37203 AN: 151876 Hom.: 5493 Cov.: 31

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.324

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.245 AC: 37208 AN: 151994 Hom.: 5493 Cov.: 31 AF XY: 0.244 AC XY: 18125 AN XY: 74282

African (AFR) AF: 0.0651 AC: 2699 AN: 41484

American (AMR) AF: 0.297 AC: 4527 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1235 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1770 AN: 5148

South Asian (SAS) AF: 0.172 AC: 828 AN: 4816

European-Finnish (FIN) AF: 0.322 AC: 3398 AN: 10554

Middle Eastern (MID) AF: 0.321 AC: 93 AN: 290

European-Non Finnish (NFE) AF: 0.320 AC: 21773 AN: 67952

Other (OTH) AF: 0.283 AC: 597 AN: 2110

Alfa AF: 0.251 Hom.: 843

Bravo AF: 0.236

Asia WGS AF: 0.254 AC: 882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.89
DANN	Benign	0.54
PhyloP100		-0.073
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: rs11013977; hg19: chr10-24506128;