rs12521753

Positions:

• chr5-116410870-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000503424.1	n.723-1773A>G		intron_variant, non_coding_transcript_variant		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;