rs2817056

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-35766274-C-A
• chr6-35766274-C-G
• chr6-35766274-C-T

Variant summary

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

The ENST00000403727.1(CMPK1P1):​n.367C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 281,436 control chromosomes in the GnomAD database, including 46,063 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 0.64 (31529 hom., cov: 31)
  • Exomes 𝑓: 0.45 (14534 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000403727.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMPK1P1	ENST00000403727.1	TSL:6	n.367C>A		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96994 AN: 151718 Hom.: 31498 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.448 AC: 58110 AN: 129600 Hom.: 14534 Cov.: 0 AF XY: 0.450 AC XY: 33169 AN XY: 73698

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.469 AC: 892 AN: 1900

American (AMR) AF: 0.280 AC: 2673 AN: 9540

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1462 AN: 2600

East Asian (EAS) AF: 0.230 AC: 798 AN: 3474

South Asian (SAS) AF: 0.547 AC: 12958 AN: 23706

European-Finnish (FIN) AF: 0.421 AC: 2941 AN: 6982

Middle Eastern (MID) AF: 0.598 AC: 342 AN: 572

European-Non Finnish (NFE) AF: 0.443 AC: 33010 AN: 74524

Other (OTH) AF: 0.481 AC: 3034 AN: 6302

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.639 AC: 97068 AN: 151836 Hom.: 31529 Cov.: 31 AF XY: 0.637 AC XY: 47285 AN XY: 74206

African (AFR) AF: 0.734 AC: 30376 AN: 41410

American (AMR) AF: 0.606 AC: 9248 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2138 AN: 5162

South Asian (SAS) AF: 0.713 AC: 3433 AN: 4812

European-Finnish (FIN) AF: 0.556 AC: 5838 AN: 10506

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41058 AN: 67910

Other (OTH) AF: 0.674 AC: 1420 AN: 2106

Alfa AF: 0.615 Hom.: 87032

Bravo AF: 0.638

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.9
DANN	Benign	0.54
PhyloP100		2.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2817056;

hg19: chr6-35734051;