rs7709377

Positions:

• chr5-116204876-A-G
• chr5-116204876-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016144.4(COMMD10):​c.510+70698A>G variant causes a intron change. The variant allele was found at a frequency of 0.373 in 151,936 control chromosomes in the GnomAD database, including 13,001 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 0.37 (13001 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.25

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COMMD10	NM_016144.4	c.510+70698A>G		intron_variant		ENST00000274458.9
COMMD10	NM_001308080.2	c.468+70698A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COMMD10	ENST00000274458.9	c.510+70698A>G		intron_variant		1	NM_016144.4	P1

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56525 AN: 151818 Hom.: 12971 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.373 AC: 56602 AN: 151936 Hom.: 13001 Cov.: 32 AF XY: 0.372 AC XY: 27645 AN XY: 74230

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.344

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.348

Alfa AF: 0.332 Hom.: 1262

Bravo AF: 0.385

Asia WGS AF: 0.337 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	15
DANN	Benign	0.64

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: rs7709377; hg19: chr5-115540573;