rs6058847

Positions:

• chr20-32736328-C-T

Variant summary

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

The NM_053041.3(COMMD7):​c.84+6980G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,020 control chromosomes in the GnomAD database, including 35,927 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 0.68 (35927 hom., cov: 32)
• Consequence: COMMD7 NM_053041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

COMMD7 (HGNC:16223): (COMM domain containing 7) Enables NF-kappaB binding activity. Involved in negative regulation of NF-kappaB transcription factor activity; negative regulation of transcription, DNA-templated; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in cytoplasmic vesicle. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000285382 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COMMD7	NM_053041.3	c.84+6980G>A		intron_variant		ENST00000278980.11	NP_444269.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMMD7	ENST00000278980.11	c.84+6980G>A		intron_variant		1	NM_053041.3	ENSP00000278980.6
ENSG00000285382	ENST00000646357.1	c.84+6980G>A		intron_variant				ENSP00000493768.1

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103355 AN: 151902 Hom.: 35891 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.698

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.680 AC: 103431 AN: 152020 Hom.: 35927 Cov.: 32 AF XY: 0.677 AC XY: 50296 AN XY: 74318

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.649

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.699

Alfa AF: 0.687 Hom.: 6294

Bravo AF: 0.663

Asia WGS AF: 0.580 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6058847; hg19: chr20-31324135;