15-77941494-A-G

Variant names:

• chr15-77941494-A-G
• rs200335579
• ENST00000563867.5:n.328T>C

Variant summary

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

The NR_157580.1(COMMD4P1):​n.434T>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 0.00123 in 1,610,168 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00099 (1 hom., cov: 30)
  • Exomes 𝑓: 0.0013 (32 hom.)
• Consequence: COMMD4P1 NR_157580.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0300

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BP6: Variant 15-77941494-A-G is Benign according to our data. Variant chr15-77941494-A-G is described in ClinVar as [Benign]. Clinvar id is 2645599.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAdExome4 at 32 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COMMD4P1	NR_157580.1	n.434T>C		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD4P1	ENST00000563867.5	n.328T>C		non_coding_transcript_exon_variant	Exon 5 of 5	6

Frequencies

GnomAD3 genomes AF: 0.000999 AC: 152 AN: 152186 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.0000724

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00144

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00236 AC: 574 AN: 242742 Hom.: 6 AF XY: 0.00296 AC XY: 390 AN XY: 131586

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000350

Gnomad ASJ exome AF: 0.00961

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0133

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000479

Gnomad OTH exome AF: 0.00220

GnomAD4 exome AF: 0.00126 AC: 1834 AN: 1457866 Hom.: 32 Cov.: 31 AF XY: 0.00163 AC XY: 1182 AN XY: 725048

Gnomad4 AFR exome AF: 0.0000899

Gnomad4 AMR exome AF: 0.000359

Gnomad4 ASJ exome AF: 0.0104

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0132

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.000239

Gnomad4 OTH exome AF: 0.00203

GnomAD4 genome AF: 0.000991 AC: 151 AN: 152302 Hom.: 1 Cov.: 30 AF XY: 0.00101 AC XY: 75 AN XY: 74462

Gnomad4 AFR AF: 0.0000722

Gnomad4 AMR AF: 0.00144

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000397

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00179 Hom.: 0

Bravo AF: 0.000646

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CSPG4P13: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	0.0070
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200335579; hg19: chr15-78233836;