rs7709377

Variant names:

• chr5-116204876-A-G
• rs7709377
• NM_016144.4:c.510+70698A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-116204876-A-G
• chr5-116204876-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016144.4(COMMD10):​c.510+70698A>G variant causes a intron change. The variant allele was found at a frequency of 0.373 in 151,936 control chromosomes in the GnomAD database, including 13,001 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 0.37 (13001 hom., cov: 32)
• Consequence: COMMD10 NM_016144.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.25
• Publications: 7 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.21).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016144.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	NM_016144.4	MANE Select	c.510+70698A>G		intron	N/A	NP_057228.1	Q9Y6G5
	COMMD10	NM_001308080.2		c.468+70698A>G		intron	N/A	NP_001295009.1	D6RJ90

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COMMD10	ENST00000274458.9	TSL:1 MANE Select	c.510+70698A>G		intron	N/A	ENSP00000274458.4	Q9Y6G5
	COMMD10	ENST00000632434.1	TSL:1	c.468+70698A>G		intron	N/A	ENSP00000488332.1	D6RJ90
	COMMD10	ENST00000515539.5	TSL:3	c.468+70698A>G		intron	N/A	ENSP00000427319.1	D6RJ90

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56525 AN: 151818 Hom.: 12971 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.373 AC: 56602 AN: 151936 Hom.: 13001 Cov.: 32 AF XY: 0.372 AC XY: 27645 AN XY: 74230

African (AFR) AF: 0.658 AC: 27258 AN: 41418

American (AMR) AF: 0.297 AC: 4530 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1776 AN: 5168

South Asian (SAS) AF: 0.227 AC: 1092 AN: 4814

European-Finnish (FIN) AF: 0.315 AC: 3318 AN: 10550

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16610 AN: 67962

Other (OTH) AF: 0.348 AC: 734 AN: 2108

Alfa AF: 0.345 Hom.: 1417

Bravo AF: 0.385

Asia WGS AF: 0.337 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.21
CADD	Benign	15
DANN	Benign	0.64
PhyloP100		5.2
Mutation Taster		=99/1	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7709377; hg19: chr5-115540573;