rs4283832

Positions:

• chr5-116232396-G-A
• chr5-116232396-G-C
• chr5-116232396-G-T

Variant summary

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

The NM_016144.4(COMMD10):​c.511-59121G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.649 in 151,650 control chromosomes in the GnomAD database, including 35,028 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 0.65 (35028 hom., cov: 30)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

Genes affected

COMMD10 (HGNC:30201): (COMM domain containing 10) Located in nucleoplasm. [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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COMMD10	NM_016144.4	c.511-59121G>A		intron_variant		ENST00000274458.9
COMMD10	NM_001308080.2	c.469-59121G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COMMD10	ENST00000274458.9	c.511-59121G>A		intron_variant		1	NM_016144.4	P1

Frequencies

GnomAD3 genomes AF: 0.649 AC: 98340 AN: 151534 Hom.: 35019 Cov.: 30

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.649 AC: 98379 AN: 151650 Hom.: 35028 Cov.: 30 AF XY: 0.650 AC XY: 48208 AN XY: 74124

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.803

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.685

Alfa AF: 0.751 Hom.: 42361

Bravo AF: 0.635

Asia WGS AF: 0.733 AC: 2547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.48
DANN	Benign	0.75

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: rs4283832; hg19: chr5-115568093;