rs6119279

chr20-32742806-A-Gchr20-32742806-A-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+502T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,836 control chromosomes in the GnomAD database, including 27,763 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 0.58 (27763 hom., cov: 30)
• Consequence: COMMD7 NM_053041.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.484

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COMMD7	NM_053041.3	c.84+502T>C		intron_variant		ENST00000278980.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COMMD7	ENST00000278980.11	c.84+502T>C		intron_variant		1	NM_053041.3	P4
COMMD7	ENST00000446419.6	c.84+502T>C		intron_variant		2		A1
COMMD7	ENST00000474815.2	c.84+502T>C		intron_variant		5
COMMD7	ENST00000610160.1	c.85-241T>C		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87673 AN: 151718 Hom.: 27716 Cov.: 30

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.578 AC: 87774 AN: 151836 Hom.: 27763 Cov.: 30 AF XY: 0.583 AC XY: 43215 AN XY: 74186

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.523

Alfa AF: 0.510 Hom.: 2641

Bravo AF: 0.600

Asia WGS AF: 0.754 AC: 2622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.6
Dann	Benign	0.43

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: rs6119279; hg19: chr20-31330612;