rs1605141

Variant names:

• chr5-91624144-G-A
• rs1605141
• ENST00000778568.1:n.776+13318G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-91624144-G-A
• chr5-91624144-G-C

Variant summary

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

The ENST00000778568.1(ARRDC3-AS1):​n.776+13318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,228 control chromosomes in the GnomAD database, including 14,512 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 0.42 (14512 hom., cov: 31)
• Consequence: ARRDC3-AS1 ENST00000778568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 2 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 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
ARRDC3-AS1	ENST00000778568.1	n.776+13318G>A		intron_variant	Intron 4 of 7
ARRDC3-AS1	ENST00000778569.1	n.973-3671G>A		intron_variant	Intron 6 of 6
ARRDC3-AS1	ENST00000778570.1	n.864-3671G>A		intron_variant	Intron 5 of 5
ARRDC3-AS1	ENST00000778572.1	n.256-3671G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64074 AN: 151112 Hom.: 14514 Cov.: 31

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.498

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.424 AC: 64083 AN: 151228 Hom.: 14512 Cov.: 31 AF XY: 0.427 AC XY: 31539 AN XY: 73868

African (AFR) AF: 0.246 AC: 10171 AN: 41300

American (AMR) AF: 0.498 AC: 7532 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1542 AN: 3466

East Asian (EAS) AF: 0.546 AC: 2771 AN: 5076

South Asian (SAS) AF: 0.484 AC: 2331 AN: 4812

European-Finnish (FIN) AF: 0.497 AC: 5236 AN: 10540

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.486 AC: 32893 AN: 67616

Other (OTH) AF: 0.443 AC: 927 AN: 2094

Alfa AF: 0.454 Hom.: 2021

Bravo AF: 0.418

Asia WGS AF: 0.416 AC: 1444 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.094
DANN	Benign	0.23
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1605141; hg19: chr5-90919961;