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.

Transcripts

RefSeq

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

Ensembl

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

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 v4.3

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

Other links and lift over

dbSNP: rs2817056; hg19: chr6-35734051;