rs373575

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
RETREG1-AS1	ENST00000653650.1	n.330-22557A>G		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.743

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.667

Alfa AF: 0.657 Hom.: 4016

Bravo AF: 0.663

Asia WGS AF: 0.558 AC: 1940 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	1.4
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs373575; hg19: chr5-16656386;