rs3858220

Positions:

• chr10-24417542-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5	c.554-15453A>G		intron_variant		ENST00000376454.8	NP_062536.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8	c.554-15453A>G		intron_variant		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

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.0871

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.153

Alfa AF: 0.173 Hom.: 4910

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs3858220; hg19: chr10-24706471;