chr5-116410870-A-G

Variant names:

• chr5-116410870-A-G
• rs12521753
• ENST00000503424.1:n.723-1773A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503424.1(COMMD10):​n.723-1773A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,076 control chromosomes in the GnomAD database, including 5,844 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 0.27 (5844 hom., cov: 33)
• Consequence: COMMD10 ENST00000503424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503424.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000503424.1	TSL:5	n.723-1773A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40978 AN: 151958 Hom.: 5822 Cov.: 33

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.270 AC: 41036 AN: 152076 Hom.: 5844 Cov.: 33 AF XY: 0.275 AC XY: 20458 AN XY: 74348

African (AFR) AF: 0.304 AC: 12613 AN: 41480

American (AMR) AF: 0.354 AC: 5413 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 891 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2299 AN: 5154

South Asian (SAS) AF: 0.278 AC: 1339 AN: 4810

European-Finnish (FIN) AF: 0.204 AC: 2164 AN: 10584

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15469 AN: 67992

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.245 Hom.: 8080

Bravo AF: 0.282

Asia WGS AF: 0.357 AC: 1237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.65
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs12521753; hg19: chr5-115746567;