5-116294307-T-G

Variant names:

• chr5-116294307-T-G
• rs37181
• ENST00000503424.1:n.104+1747T>G

Variant summary

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

The ENST00000508250.5(COMMD10):​n.148+1747T>G variant causes a intron 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 ENST00000508250.5 intron
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COMMD10	ENST00000503424.1	n.104+1747T>G		intron_variant	Intron 1 of 5	5
COMMD10	ENST00000508250.5	n.148+1747T>G		intron_variant	Intron 2 of 4	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;