rs3858220

Variant names:

• chr10-24417542-A-G
• rs3858220
• NM_019590.5:c.554-15453A>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.554-15453A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,154 control chromosomes in the GnomAD database, including 1,994 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 0.16 (1994 hom., cov: 32)
• Consequence: KIAA1217 NM_019590.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-15453A>G		intron_variant	Intron 3 of 20	ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-15453A>G		intron_variant	Intron 3 of 20	1	NM_019590.5	ENSP00000365637.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24240 AN: 152036 Hom.: 1979 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.0874

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.160 AC: 24283 AN: 152154 Hom.: 1994 Cov.: 32 AF XY: 0.158 AC XY: 11725 AN XY: 74360

African (AFR) AF: 0.112 AC: 4657 AN: 41526

American (AMR) AF: 0.177 AC: 2704 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3472

East Asian (EAS) AF: 0.197 AC: 1014 AN: 5156

South Asian (SAS) AF: 0.0871 AC: 420 AN: 4822

European-Finnish (FIN) AF: 0.196 AC: 2074 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12407 AN: 67994

Other (OTH) AF: 0.153 AC: 323 AN: 2112

Alfa AF: 0.173 Hom.: 10512

Bravo AF: 0.159

Asia WGS AF: 0.146 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.75
DANN	Benign	0.53
PhyloP100		-1.2
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: rs3858220; hg19: chr10-24706471;