Variant rs2275247 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_024874.5(KIAA0319L):c.2779+56A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 1,610,572 control chromosomes in the GnomAD database, including 37,155 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 0.26 ( 10563 hom., cov: 32)

Exomes 𝑓: 0.090 ( 26592 hom. )

Consequence

KIAA0319L
NM_024874.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.514

Variant links:

Genes affected

KIAA0319L (HGNC:30071): (KIAA0319 like) Predicted to act upstream of or within several processes, including flagellated sperm motility; proacrosomal vesicle fusion; and receptor-mediated endocytosis of virus by host cell. Located in Golgi apparatus; cytoplasmic vesicle; and nucleolus. [provided by Alliance of Genome Resources, Apr 2022]

KIAA0319L 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=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIAA0319L	NM_024874.5 linkuse as main transcript	c.2779+56A>G		intron_variant		ENST00000325722.8	NP_079150.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIAA0319L	ENST00000325722.8 linkuse as main transcript	c.2779+56A>G		intron_variant		1	NM_024874.5	ENSP00000318406	P1	Q8IZA0-1

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39025

AN:

152072

Hom.:

10513

Cov.:

show subpopulations

Gnomad AFR

AF:

0.610

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.317

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.776

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.0998

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0317

Gnomad OTH

AF:

0.225

GnomAD4 exome

AF:

0.0903

AC:

131730

AN:

1458382

Hom.:

26592

AF XY:

0.0899

AC XY:

65270

AN XY:

725648

show subpopulations

Gnomad4 AFR exome

AF:

0.630

Gnomad4 AMR exome

AF:

0.387

Gnomad4 ASJ exome

AF:

0.0451

Gnomad4 EAS exome

AF:

0.789

Gnomad4 SAS exome

AF:

0.194

Gnomad4 FIN exome

AF:

0.0997

Gnomad4 NFE exome

AF:

0.0274

Gnomad4 OTH exome

AF:

0.135

GnomAD4 genome

AF:

0.257

AC:

39141

AN:

152190

Hom.:

10563

Cov.:

AF XY:

0.263

AC XY:

19546

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.610

Gnomad4 AMR

AF:

0.318

Gnomad4 ASJ

AF:

0.0421

Gnomad4 EAS

AF:

0.775

Gnomad4 SAS

AF:

0.224

Gnomad4 FIN

AF:

0.0998

Gnomad4 NFE

AF:

0.0317

Gnomad4 OTH

AF:

0.226

Alfa

AF:

0.0838

Hom.:

3799

Bravo

AF:

0.292

Asia WGS

AF:

0.499

AC:

1733

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.2

DANN

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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