rs373575

Variant names:

• chr5-16656277-A-G
• rs373575
• ENST00000653650.1:n.330-22557A>G

Variant summary

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

The ENST00000653650.1(RETREG1-AS1):​n.330-22557A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,288 control chromosomes in the GnomAD database, including 33,039 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 0.66 (33039 hom., cov: 29)
• Consequence: RETREG1-AS1 ENST00000653650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 1 publications found

Genes affected

RETREG1-AS1 (HGNC:55551): (RETREG1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.736 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653650.1. 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
	RETREG1-AS1	ENST00000653650.1		n.330-22557A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.659 AC: 99673 AN: 151176 Hom.: 32987 Cov.: 29

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.660 AC: 99778 AN: 151288 Hom.: 33039 Cov.: 29 AF XY: 0.658 AC XY: 48593 AN XY: 73814

African (AFR) AF: 0.743 AC: 30647 AN: 41222

American (AMR) AF: 0.636 AC: 9674 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2436 AN: 3466

East Asian (EAS) AF: 0.496 AC: 2524 AN: 5090

South Asian (SAS) AF: 0.641 AC: 3073 AN: 4792

European-Finnish (FIN) AF: 0.594 AC: 6169 AN: 10378

Middle Eastern (MID) AF: 0.664 AC: 194 AN: 292

European-Non Finnish (NFE) AF: 0.635 AC: 43097 AN: 67846

Other (OTH) AF: 0.667 AC: 1401 AN: 2100

Alfa AF: 0.650 Hom.: 9397

Bravo AF: 0.663

Asia WGS AF: 0.558 AC: 1940 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		-0.57

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: rs373575;

hg19: chr5-16656386;