Variant rs3818672 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_019590.5(KIAA1217):c.1680-36C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 1,553,722 control chromosomes in the GnomAD database, including 38,737 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 0.25 ( 5381 hom., cov: 32)

Exomes 𝑓: 0.21 ( 33356 hom. )

Consequence

KIAA1217
NM_019590.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.44

Variant links:

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]

KIAA1217 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.66).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA1217	NM_019590.5 link	c.1680-36C>A		intron_variant		ENST00000376454.8	NP_062536.2	Q5T5P2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA1217	ENST00000376454.8 link	c.1680-36C>A		intron_variant		1	NM_019590.5	ENSP00000365637.3		Q5T5P2-1

Frequencies

GnomAD3 genomes

AF:

0.249

AC:

37760

AN:

151658

Hom.:

5364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.363

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.239

Gnomad ASJ

AF:

0.205

Gnomad EAS

AF:

0.349

Gnomad SAS

AF:

0.380

Gnomad FIN

AF:

0.125

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.238

AC:

59307

AN:

249068

Hom.:

7795

AF XY:

0.240

AC XY:

32369

AN XY:

134708

show subpopulations

Gnomad AFR exome

AF:

0.365

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.208

Gnomad EAS exome

AF:

0.355

Gnomad SAS exome

AF:

0.373

Gnomad FIN exome

AF:

0.129

Gnomad NFE exome

AF:

0.187

Gnomad OTH exome

AF:

0.231

GnomAD4 exome

AF:

0.208

AC:

291256

AN:

1401944

Hom.:

33356

Cov.:

AF XY:

0.212

AC XY:

148977

AN XY:

701138

show subpopulations

Gnomad4 AFR exome

AF:

0.371

Gnomad4 AMR exome

AF:

0.241

Gnomad4 ASJ exome

AF:

0.203

Gnomad4 EAS exome

AF:

0.358

Gnomad4 SAS exome

AF:

0.370

Gnomad4 FIN exome

AF:

0.135

Gnomad4 NFE exome

AF:

0.185

Gnomad4 OTH exome

AF:

0.234

GnomAD4 genome

AF:

0.249

AC:

37817

AN:

151778

Hom.:

5381

Cov.:

AF XY:

0.247

AC XY:

18358

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.363

Gnomad4 AMR

AF:

0.239

Gnomad4 ASJ

AF:

0.205

Gnomad4 EAS

AF:

0.348

Gnomad4 SAS

AF:

0.380

Gnomad4 FIN

AF:

0.125

Gnomad4 NFE

AF:

0.189

Gnomad4 OTH

AF:

0.270

Alfa

AF:

0.221

Hom.:

915

Bravo

AF:

0.264

Asia WGS

AF:

0.388

AC:

1346

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.61

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over