rs503425

Positions:

• chr11-118822018-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532177.1(COX7CP3):​n.124T>C 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 0.21 in 151,336 control chromosomes in the GnomAD database, including 3,510 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 0.21 (3510 hom., cov: 28)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: COX7CP3 ENST00000532177.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

COX7CP3 (HGNC:56511): (COX7C pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COX7CP3	ENST00000532177.1	n.124T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31815 AN: 151218 Hom.: 3505 Cov.: 28

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.225

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 12 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 8

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.210 AC: 31836 AN: 151336 Hom.: 3510 Cov.: 28 AF XY: 0.213 AC XY: 15741 AN XY: 73874

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.355

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.228

Alfa AF: 0.197 Hom.: 801

Bravo AF: 0.206

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs503425; hg19: chr11-118692727;