rs12521753

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000503424.1	n.723-1773A>G		intron_variant	Intron 5 of 5	5

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

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.446

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.285

Alfa AF: 0.241 Hom.: 6139

Bravo AF: 0.282

Asia WGS AF: 0.357 AC: 1237 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12521753; hg19: chr5-115746567;