chr5-91685570-A-G

Variant names:

• chr5-91685570-A-G
• rs13153333
• ENST00000651690.1:n.174-35469A>G

Variant summary

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

The ENST00000651690.1(ENSG00000286121):​n.174-35469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.032 in 152,204 control chromosomes in the GnomAD database, including 93 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 0.032 (93 hom., cov: 32)
• Consequence: ENSG00000286121 ENST00000651690.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02
• Publications: 5 publications found

Genes affected

ENSG00000286121 (HGNC:):

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=-0.76).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.032 (4874/152204) while in subpopulation NFE AF = 0.0494 (3360/67964). AF 95% confidence interval is 0.048. There are 93 homozygotes in GnomAd4. There are 2209 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 93 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
ENSG00000286121	ENST00000651690.1	n.174-35469A>G		intron_variant	Intron 1 of 8
ARRDC3-AS1	ENST00000778568.1	n.886-1907A>G		intron_variant	Intron 5 of 7

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4873 AN: 152086 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00939

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0320 AC: 4874 AN: 152204 Hom.: 93 Cov.: 32 AF XY: 0.0297 AC XY: 2209 AN XY: 74416

African (AFR) AF: 0.00936 AC: 389 AN: 41550

American (AMR) AF: 0.0263 AC: 402 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4830

European-Finnish (FIN) AF: 0.0370 AC: 392 AN: 10604

Middle Eastern (MID) AF: 0.0616 AC: 18 AN: 292

European-Non Finnish (NFE) AF: 0.0494 AC: 3360 AN: 67964

Other (OTH) AF: 0.0303 AC: 64 AN: 2114

Alfa AF: 0.0456 Hom.: 279

Bravo AF: 0.0312

Asia WGS AF: 0.0110 AC: 38 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.71
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs13153333; hg19: chr5-90981387;