5-116294307-T-G

Position:

• chr5-116294307-T-G

Variant summary

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

The ENST00000503424.1(COMMD10):​n.104+1747T>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 0.339 in 151,848 control chromosomes in the GnomAD database, including 10,314 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 0.34 (10314 hom., cov: 32)
• Consequence: COMMD10 ENST00000503424.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

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=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 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.104+1747T>G		intron_variant, non_coding_transcript_variant		5
COMMD10	ENST00000508250.5	n.148+1747T>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.339 AC: 51377 AN: 151730 Hom.: 10293 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.339 AC: 51445 AN: 151848 Hom.: 10314 Cov.: 32 AF XY: 0.338 AC XY: 25108 AN XY: 74184

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.233

Gnomad4 OTH AF: 0.326

Alfa AF: 0.232 Hom.: 2141

Bravo AF: 0.354

Asia WGS AF: 0.387 AC: 1343 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	13
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37181; hg19: chr5-115630004;