Variant chr19-1969478-G-T details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001319.7(CSNK1G2):c.-265-30G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 240,688 control chromosomes in the GnomAD database, including 27,784 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 0.49 ( 19249 hom., cov: 29)

Exomes 𝑓: 0.42 ( 8535 hom. )

Consequence

CSNK1G2
NM_001319.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.189

Variant links:

Genes affected

CSNK1G2 (HGNC:2455): (casein kinase 1 gamma 2) Enables protein serine/threonine kinase activity. Involved in peptidyl-serine phosphorylation. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

CSNK1G2 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CSNK1G2	NM_001319.7 linkuse as main transcript	c.-265-30G>T		intron_variant		ENST00000255641.13	NP_001310.3

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
CSNK1G2	ENST00000255641.13 linkuse as main transcript	c.-265-30G>T	intron_variant	1	NM_001319.7	ENSP00000255641	P1
CSNK1G2	ENST00000589350.2 linkuse as main transcript	c.-265-30G>T	intron_variant	5		ENSP00000465106
CSNK1G2	ENST00000591752.5 linkuse as main transcript	c.-265-30G>T	intron_variant	5		ENSP00000467214
CSNK1G2	ENST00000614707.1 linkuse as main transcript	n.96-30G>T	intron_variant, non_coding_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.487

AC:

73799

AN:

151536

Hom.:

19221

Cov.:

show subpopulations

Gnomad AFR

AF:

0.653

Gnomad AMI

AF:

0.344

Gnomad AMR

AF:

0.464

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.701

Gnomad SAS

AF:

0.514

Gnomad FIN

AF:

0.413

Gnomad MID

AF:

0.383

Gnomad NFE

AF:

0.385

Gnomad OTH

AF:

0.471

GnomAD4 exome

AF:

0.424

AC:

37775

AN:

89034

Hom.:

8535

Cov.:

AF XY:

0.422

AC XY:

18827

AN XY:

44616

show subpopulations

Gnomad4 AFR exome

AF:

0.669

Gnomad4 AMR exome

AF:

0.458

Gnomad4 ASJ exome

AF:

0.519

Gnomad4 EAS exome

AF:

0.626

Gnomad4 SAS exome

AF:

0.514

Gnomad4 FIN exome

AF:

0.396

Gnomad4 NFE exome

AF:

0.376

Gnomad4 OTH exome

AF:

0.441

GnomAD4 genome

AF:

0.487

AC:

73875

AN:

151654

Hom.:

19249

Cov.:

AF XY:

0.491

AC XY:

36337

AN XY:

74074

show subpopulations

Gnomad4 AFR

AF:

0.653

Gnomad4 AMR

AF:

0.465

Gnomad4 ASJ

AF:

0.534

Gnomad4 EAS

AF:

0.702

Gnomad4 SAS

AF:

0.513

Gnomad4 FIN

AF:

0.413

Gnomad4 NFE

AF:

0.385

Gnomad4 OTH

AF:

0.472

Alfa

AF:

0.275

Hom.:

610

Bravo

AF:

0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.80

DANN

Benign

0.65

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