chr5-116176655-G-A

Position:

• chr5-116176655-G-A

Variant summary

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

The NM_016144.4(COMMD10):​c.510+42477G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,668 control chromosomes in the GnomAD database, including 10,212 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 0.31 (10212 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

Genes affected

COMMD10 (HGNC:30201): (COMM domain containing 10) Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

COMMD10 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COMMD10	NM_016144.4	c.510+42477G>A		intron_variant		ENST00000274458.9	NP_057228.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000274458.9	c.510+42477G>A		intron_variant		1	NM_016144.4	ENSP00000274458.4

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47032 AN: 151550 Hom.: 10189 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.311 AC: 47103 AN: 151668 Hom.: 10212 Cov.: 32 AF XY: 0.309 AC XY: 22872 AN XY: 74106

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.286

Alfa AF: 0.203 Hom.: 3924

Bravo AF: 0.332

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.40

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: rs1396485; hg19: chr5-115512352;