NM_019590.5:c.355-73815C>T

Variant names:

• chr10-24307054-C-T
• rs10828624
• NM_019590.5:c.355-73815C>T

Variant summary

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

The NM_019590.5(KIAA1217):​c.355-73815C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,206 control chromosomes in the GnomAD database, including 5,175 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 0.21 (5175 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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.355-73815C>T		intron	N/A	NP_062536.2
	KIAA1217	NM_001282767.2		c.355-73815C>T		intron	N/A	NP_001269696.1
	KIAA1217	NM_001282768.2		c.355-73815C>T		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.355-73815C>T		intron	N/A	ENSP00000365637.3
	KIAA1217	ENST00000376452.7	TSL:1	c.355-73815C>T		intron	N/A	ENSP00000365635.3
	KIAA1217	ENST00000458595.5	TSL:1	c.355-73815C>T		intron	N/A	ENSP00000392625.1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31400 AN: 152088 Hom.: 5157 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0980

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.207 AC: 31464 AN: 152206 Hom.: 5175 Cov.: 32 AF XY: 0.205 AC XY: 15266 AN XY: 74444

African (AFR) AF: 0.433 AC: 17945 AN: 41478

American (AMR) AF: 0.112 AC: 1718 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3472

East Asian (EAS) AF: 0.387 AC: 2006 AN: 5178

South Asian (SAS) AF: 0.346 AC: 1670 AN: 4822

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10612

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0980 AC: 6664 AN: 68022

Other (OTH) AF: 0.193 AC: 408 AN: 2114

Alfa AF: 0.137 Hom.: 4013

Bravo AF: 0.220

Asia WGS AF: 0.350 AC: 1214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.48
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: rs10828624; hg19: chr10-24595983;