19-1969478-G-T

Variant names:

• chr19-1969478-G-T
• rs2074882
• NM_001319.7:c.-265-30G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001319.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G2	NM_001319.7	MANE Select	c.-265-30G>T		intron	N/A	NP_001310.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK1G2	ENST00000255641.13	TSL:1 MANE Select	c.-265-30G>T		intron	N/A	ENSP00000255641.7
	CSNK1G2	ENST00000935020.1		c.-295G>T		5_prime_UTR_premature_start_codon_gain	Exon 2 of 12	ENSP00000605079.1
	CSNK1G2	ENST00000935020.1		c.-295G>T		5_prime_UTR	Exon 2 of 12	ENSP00000605079.1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73799 AN: 151536 Hom.: 19221 Cov.: 29

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.: 0 AF XY: 0.422 AC XY: 18827 AN XY: 44616

African (AFR) AF: 0.669 AC: 2111 AN: 3154

American (AMR) AF: 0.458 AC: 1133 AN: 2474

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1997 AN: 3848

East Asian (EAS) AF: 0.626 AC: 4982 AN: 7956

South Asian (SAS) AF: 0.514 AC: 409 AN: 796

European-Finnish (FIN) AF: 0.396 AC: 2166 AN: 5476

Middle Eastern (MID) AF: 0.368 AC: 198 AN: 538

European-Non Finnish (NFE) AF: 0.376 AC: 22055 AN: 58610

Other (OTH) AF: 0.441 AC: 2724 AN: 6182

GnomAD4 genome AF: 0.487 AC: 73875 AN: 151654 Hom.: 19249 Cov.: 29 AF XY: 0.491 AC XY: 36337 AN XY: 74074

African (AFR) AF: 0.653 AC: 26973 AN: 41336

American (AMR) AF: 0.465 AC: 7081 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1849 AN: 3462

East Asian (EAS) AF: 0.702 AC: 3585 AN: 5110

South Asian (SAS) AF: 0.513 AC: 2456 AN: 4786

European-Finnish (FIN) AF: 0.413 AC: 4354 AN: 10532

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26157 AN: 67878

Other (OTH) AF: 0.472 AC: 993 AN: 2104

Alfa AF: 0.275 Hom.: 610

Bravo AF: 0.499

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.80
DANN	Benign	0.65
PhyloP100		-0.19
PromoterAI		-0.0064	Neutral
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: rs2074882; hg19: chr19-1969477;