rs1997791

Variant names:

• chr20-50479891-C-A
• rs1997791
• ENST00000444980.1:n.125C>A

Your query was ambiguous. Multiple possible variants found:

• chr20-50479891-C-A
• chr20-50479891-C-G

Variant summary

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

The ENST00000444980.1(COX6CP2):​n.125C>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 0.76 in 181,688 control chromosomes in the GnomAD database, including 52,750 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 0.76 (43831 hom., cov: 32)
  • Exomes 𝑓: 0.78 (8919 hom.)
• Consequence: COX6CP2 ENST00000444980.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 5 publications found

Genes affected

COX6CP2 (HGNC:16600): (cytochrome c oxidase subunit 6C pseudogene 2)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COX6CP2		n.50479891C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COX6CP2	ENST00000444980.1	n.125C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.757 AC: 115103 AN: 151952 Hom.: 43820 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.806

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.748

GnomAD4 exome AF: 0.777 AC: 23012 AN: 29618 Hom.: 8919 Cov.: 0 AF XY: 0.779 AC XY: 14713 AN XY: 18892

African (AFR) AF: 0.787 AC: 288 AN: 366

American (AMR) AF: 0.873 AC: 534 AN: 612

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 351 AN: 460

East Asian (EAS) AF: 0.579 AC: 483 AN: 834

South Asian (SAS) AF: 0.820 AC: 4182 AN: 5100

European-Finnish (FIN) AF: 0.808 AC: 1920 AN: 2376

Middle Eastern (MID) AF: 0.810 AC: 81 AN: 100

European-Non Finnish (NFE) AF: 0.770 AC: 14140 AN: 18358

Other (OTH) AF: 0.732 AC: 1033 AN: 1412

GnomAD4 genome AF: 0.757 AC: 115158 AN: 152070 Hom.: 43831 Cov.: 32 AF XY: 0.759 AC XY: 56430 AN XY: 74334

African (AFR) AF: 0.780 AC: 32328 AN: 41466

American (AMR) AF: 0.805 AC: 12303 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2585 AN: 3468

East Asian (EAS) AF: 0.551 AC: 2845 AN: 5162

South Asian (SAS) AF: 0.805 AC: 3883 AN: 4824

European-Finnish (FIN) AF: 0.801 AC: 8471 AN: 10570

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50322 AN: 67988

Other (OTH) AF: 0.740 AC: 1562 AN: 2112

Alfa AF: 0.746 Hom.: 30542

Bravo AF: 0.757

Asia WGS AF: 0.695 AC: 2421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1997791; hg19: chr20-49096428;