5-91428781-T-C

Variant names:

• chr5-91428781-T-C
• rs6862125
• ENST00000630823.3:n.591+10010T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000630823.3(ARRDC3-AS1):​n.591+10010T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,074 control chromosomes in the GnomAD database, including 6,105 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 0.25 (6105 hom., cov: 32)
• Consequence: ARRDC3-AS1 ENST00000630823.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 10 publications found

Genes affected

ARRDC3-AS1 (HGNC:44145): (ARRDC3 antisense RNA 1)

ENSG00000301415 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000630823.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARRDC3-AS1	ENST00000630823.3	TSL:3	n.591+10010T>C		intron	N/A
	ARRDC3-AS1	ENST00000656345.1		n.473+10010T>C		intron	N/A
	ARRDC3-AS1	ENST00000664873.1		n.138+10010T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38638 AN: 151956 Hom.: 6087 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.254 AC: 38691 AN: 152074 Hom.: 6105 Cov.: 32 AF XY: 0.258 AC XY: 19154 AN XY: 74362

African (AFR) AF: 0.409 AC: 16950 AN: 41456

American (AMR) AF: 0.227 AC: 3465 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3466

East Asian (EAS) AF: 0.524 AC: 2699 AN: 5148

South Asian (SAS) AF: 0.417 AC: 2008 AN: 4820

European-Finnish (FIN) AF: 0.135 AC: 1432 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10866 AN: 67994

Other (OTH) AF: 0.227 AC: 480 AN: 2110

Alfa AF: 0.195 Hom.: 10901

Bravo AF: 0.262

Asia WGS AF: 0.444 AC: 1542 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.38
DANN	Benign	0.31
PhyloP100		-0.79

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6862125;

hg19: chr5-90724598;