rs750062577

Variant names:

• chr20-478765-CAAAAAAAA-C
• rs750062577
• NM_177559.3:c.*5188_*5195delTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr20-478765-CAAAAAAAA-C
• chr20-478765-CAAAAAAAA-CA
• chr20-478765-CAAAAAAAA-CAA
• chr20-478765-CAAAAAAAA-CAAA
• chr20-478765-CAAAAAAAA-CAAAA
• chr20-478765-CAAAAAAAA-CAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAAAAAA
• chr20-478765-CAAAAAAAA-CAAAAAAAAAAAAAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000400227.8(CSNK2A1):​c.1061-13_1061-6delTTTTTTTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000307 in 175,854 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00024 (0 hom., cov: 27)
  • Exomes 𝑓: 0.00044 (0 hom.)
• Consequence: CSNK2A1 ENST00000400227.8 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.725

Genes affected

CSNK2A1 (HGNC:2457): (casein kinase 2 alpha 1) Casein kinase II is a serine/threonine protein kinase that phosphorylates acidic proteins such as casein. It is involved in various cellular processes, including cell cycle control, apoptosis, and circadian rhythm. The kinase exists as a tetramer and is composed of an alpha, an alpha-prime, and two beta subunits. The alpha subunits contain the catalytic activity while the beta subunits undergo autophosphorylation. The protein encoded by this gene represents the alpha subunit. Multiple transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Apr 2018]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000237 (27/113954) while in subpopulation NFE AF= 0.000211 (11/52164). AF 95% confidence interval is 0.000118. There are 0 homozygotes in gnomad4. There are 13 alleles in male gnomad4 subpopulation. Median coverage is 27. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 27 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A1	NM_177559.3	c.*5188_*5195delTTTTTTTT		3_prime_UTR_variant	Exon 14 of 14	ENST00000217244.9	NP_808227.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A1	ENST00000217244	c.*5188_*5195delTTTTTTTT		3_prime_UTR_variant	Exon 14 of 14	1	NM_177559.3	ENSP00000217244.3

Frequencies

GnomAD3 genomes AF: 0.000237 AC: 27 AN: 113954 Hom.: 0 Cov.: 27

Gnomad AFR AF: 0.0000636

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00229

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000211

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000436 AC: 27 AN: 61900 Hom.: 0 AF XY: 0.000274 AC XY: 10 AN XY: 36464

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00390

Gnomad4 NFE exome AF: 0.000294

Gnomad4 OTH exome AF: 0.000739

GnomAD4 genome AF: 0.000237 AC: 27 AN: 113954 Hom.: 0 Cov.: 27 AF XY: 0.000240 AC XY: 13 AN XY: 54230

Gnomad4 AFR AF: 0.0000636

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00229

Gnomad4 NFE AF: 0.000211

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs750062577; hg19: chr20-459409;