rs2183696

Variant names:

• chr10-24502452-A-G
• rs2183696
• NM_019590.5:c.2001+907A>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.2001+907A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,870 control chromosomes in the GnomAD database, including 19,931 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 0.50 (19931 hom., cov: 31)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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.2001+907A>G		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.1896+907A>G		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.1896+907A>G		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.2001+907A>G		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376451.4	TSL:1	c.1050+907A>G		intron	N/A	ENSP00000365634.2
	KIAA1217	ENST00000376452.7	TSL:1	c.1896+907A>G		intron	N/A	ENSP00000365635.3

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76229 AN: 151752 Hom.: 19892 Cov.: 31

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.503 AC: 76322 AN: 151870 Hom.: 19931 Cov.: 31 AF XY: 0.503 AC XY: 37312 AN XY: 74228

African (AFR) AF: 0.631 AC: 26138 AN: 41398

American (AMR) AF: 0.437 AC: 6674 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1683 AN: 3468

East Asian (EAS) AF: 0.349 AC: 1792 AN: 5140

South Asian (SAS) AF: 0.386 AC: 1856 AN: 4806

European-Finnish (FIN) AF: 0.549 AC: 5786 AN: 10546

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30634 AN: 67938

Other (OTH) AF: 0.477 AC: 1003 AN: 2102

Alfa AF: 0.474 Hom.: 7519

Bravo AF: 0.504

Asia WGS AF: 0.396 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.3
DANN	Benign	0.36
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		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: rs2183696; hg19: chr10-24791381;