rs10764472

Variant names:

• chr10-24464217-T-C
• rs10764472
• NM_019590.5:c.847-9011T>C

Variant summary

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

The NM_019590.5(KIAA1217):​c.847-9011T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,208 control chromosomes in the GnomAD database, including 2,151 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 0.15 (2151 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• 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]

LOC105376455 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.309 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.847-9011T>C		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.847-9011T>C		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.847-9011T>C		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.847-9011T>C		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.847-9011T>C		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.847-9011T>C		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23352 AN: 152092 Hom.: 2150 Cov.: 32

Gnomad AFR AF: 0.0746

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.153 AC: 23360 AN: 152208 Hom.: 2151 Cov.: 32 AF XY: 0.160 AC XY: 11913 AN XY: 74406

African (AFR) AF: 0.0746 AC: 3101 AN: 41578

American (AMR) AF: 0.204 AC: 3121 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1652 AN: 5156

South Asian (SAS) AF: 0.322 AC: 1550 AN: 4810

European-Finnish (FIN) AF: 0.141 AC: 1496 AN: 10602

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.166 AC: 11277 AN: 67996

Other (OTH) AF: 0.184 AC: 389 AN: 2112

Alfa AF: 0.165 Hom.: 4339

Bravo AF: 0.152

Asia WGS AF: 0.312 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		-0.27
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: rs10764472; hg19: chr10-24753146;