rs503425

Variant names:

• chr11-118822018-T-C
• rs503425
• ENST00000532177.1:n.124T>C

Variant summary

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

The ENST00000816807.1(ENSG00000306294):​n.304T>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: ENSG00000306294 ENST00000816807.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 11 publications found

Genes affected

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

ENSG00000306294 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816807.1. 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
	COX7CP3	ENST00000532177.1	TSL:6	n.124T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000306294	ENST00000816807.1		n.304T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000306274	ENST00000816613.1		n.125-4508A>G		intron	N/A

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 6

Other (OTH) AF: 0.00 AC: 0 AN: 2

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

African (AFR) AF: 0.223 AC: 9192 AN: 41222

American (AMR) AF: 0.157 AC: 2367 AN: 15120

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 709 AN: 3464

East Asian (EAS) AF: 0.317 AC: 1631 AN: 5138

South Asian (SAS) AF: 0.355 AC: 1688 AN: 4752

European-Finnish (FIN) AF: 0.202 AC: 2115 AN: 10468

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13385 AN: 67874

Other (OTH) AF: 0.228 AC: 478 AN: 2092

Alfa AF: 0.197 Hom.: 823

Bravo AF: 0.206

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.9
DANN	Benign	0.63
PhyloP100		1.4

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: rs503425;

hg19: chr11-118692727;