6-35766274-C-G

Variant names:

• chr6-35766274-C-G
• rs2817056
• ENST00000403727.1:n.367C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000403727.1(CMPK1P1):​n.367C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CMPK1P1 ENST00000403727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48
• Publications: 8 publications found

Genes affected

CMPK1P1 (HGNC:56924):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CMPK1P1		n.35766274C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CMPK1P1	ENST00000403727.1	n.367C>G		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 137150 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 78520

African (AFR) AF: 0.00 AC: 0 AN: 2032

American (AMR) AF: 0.00 AC: 0 AN: 10106

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2744

East Asian (EAS) AF: 0.00 AC: 0 AN: 3662

South Asian (SAS) AF: 0.00 AC: 0 AN: 24924

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7226

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 574

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 79244

Other (OTH) AF: 0.00 AC: 0 AN: 6638

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	8.0
DANN	Benign	0.42
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs2817056; hg19: chr6-35734051;