ENST00000563867.5:n.226C>T

Variant names:

• chr15-77941755-G-A
• rs117931496
• ENST00000563867.5:n.226C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The ENST00000563867.5(COMMD4P1):​n.226C>T 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 0.0078 in 1,613,836 control chromosomes in the GnomAD database, including 85 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0054 (3 hom., cov: 31)
  • Exomes 𝑓: 0.0080 (82 hom.)
• Consequence: COMMD4P1 ENST00000563867.5 non_coding_transcript_exon
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0290

Genes affected

COMMD4P1 (HGNC:51909): (COMM domain containing 4 pseudogene 1)

ENSG00000290666 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BP6: Variant 15-77941755-G-A is Benign according to our data. Variant chr15-77941755-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1879301.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD4P1	NR_157580.1	n.332C>T		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD4P1	ENST00000563867.5	n.226C>T		non_coding_transcript_exon_variant	Exon 4 of 5	6
ENSG00000290666	ENST00000568184.1	n.*144C>T		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.00545 AC: 829 AN: 152168 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.00215

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00464

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.00132

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00862

Gnomad OTH AF: 0.00621

GnomAD3 exomes AF: 0.00611 AC: 1534 AN: 251068 Hom.: 12 AF XY: 0.00612 AC XY: 830 AN XY: 135710

Gnomad AFR exome AF: 0.00166

Gnomad AMR exome AF: 0.00425

Gnomad ASJ exome AF: 0.0118

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00346

Gnomad FIN exome AF: 0.00120

Gnomad NFE exome AF: 0.00937

Gnomad OTH exome AF: 0.00751

GnomAD4 exome AF: 0.00804 AC: 11755 AN: 1461554 Hom.: 82 Cov.: 34 AF XY: 0.00792 AC XY: 5756 AN XY: 727098

Gnomad4 AFR exome AF: 0.00134

Gnomad4 AMR exome AF: 0.00441

Gnomad4 ASJ exome AF: 0.0116

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00308

Gnomad4 FIN exome AF: 0.00238

Gnomad4 NFE exome AF: 0.00928

Gnomad4 OTH exome AF: 0.00769

GnomAD4 genome AF: 0.00544 AC: 829 AN: 152282 Hom.: 3 Cov.: 31 AF XY: 0.00486 AC XY: 362 AN XY: 74460

Gnomad4 AFR AF: 0.00214

Gnomad4 AMR AF: 0.00464

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00269

Gnomad4 FIN AF: 0.00132

Gnomad4 NFE AF: 0.00862

Gnomad4 OTH AF: 0.00615

Alfa AF: 0.00573 Hom.: 1

Bravo AF: 0.00588

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CSPG4P13: BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs117931496; hg19: chr15-78234097;