chr5-16658386-A-G

Variant names:

• chr5-16658386-A-G
• rs428263
• ENST00000653650.1:n.330-20448A>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.330-20448A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.668 in 152,106 control chromosomes in the GnomAD database, including 34,172 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 0.67 (34172 hom., cov: 33)
• Consequence: RETREG1-AS1 ENST00000653650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 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.330-20448A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101550 AN: 151988 Hom.: 34113 Cov.: 33

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.674

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

GnomAD4 genome AF: 0.668 AC: 101668 AN: 152106 Hom.: 34172 Cov.: 33 AF XY: 0.668 AC XY: 49625 AN XY: 74336

African (AFR) AF: 0.763 AC: 31670 AN: 41504

American (AMR) AF: 0.640 AC: 9767 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2446 AN: 3470

East Asian (EAS) AF: 0.569 AC: 2938 AN: 5160

South Asian (SAS) AF: 0.646 AC: 3116 AN: 4824

European-Finnish (FIN) AF: 0.599 AC: 6337 AN: 10576

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43200 AN: 67988

Other (OTH) AF: 0.675 AC: 1425 AN: 2110

Alfa AF: 0.659 Hom.: 5816

Bravo AF: 0.673

Asia WGS AF: 0.586 AC: 2037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.6
DANN	Benign	0.82
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs428263; hg19: chr5-16658495;