5-116398108-G-C

Variant names:

• chr5-116398108-G-C
• rs7734156
• ENST00000503424.1:n.582-1374G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000503424.1(COMMD10):​n.582-1374G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0295 in 152,196 control chromosomes in the GnomAD database, including 81 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 0.029 (81 hom., cov: 32)
• Consequence: COMMD10 ENST00000503424.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 3 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=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0295 (4486/152196) while in subpopulation NFE AF = 0.0408 (2775/68022). AF 95% confidence interval is 0.0395. There are 81 homozygotes in GnomAd4. There are 2160 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 81 AR gene

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.582-1374G>C		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4484 AN: 152078 Hom.: 81 Cov.: 32

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0265

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0114

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0295 AC: 4486 AN: 152196 Hom.: 81 Cov.: 32 AF XY: 0.0290 AC XY: 2160 AN XY: 74410

African (AFR) AF: 0.0180 AC: 749 AN: 41498

American (AMR) AF: 0.0264 AC: 404 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.0112 AC: 54 AN: 4824

European-Finnish (FIN) AF: 0.0318 AC: 337 AN: 10586

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0408 AC: 2775 AN: 68022

Other (OTH) AF: 0.0227 AC: 48 AN: 2110

Alfa AF: 0.0214 Hom.: 11

Bravo AF: 0.0284

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.65
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7734156; hg19: chr5-115733805;