chr5-16656461-A-G

Variant names:

• chr5-16656461-A-G
• rs588367
• ENST00000653650.1:n.330-22373A>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.330-22373A>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 152,058 control chromosomes in the GnomAD database, including 33,248 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 (33248 hom., cov: 32)
• Consequence: RETREG1-AS1 ENST00000653650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574
• Publications: 5 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=-0.61).
• 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.330-22373A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100213 AN: 151938 Hom.: 33195 Cov.: 32

Gnomad AFR AF: 0.743

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.658

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: 100323 AN: 152058 Hom.: 33248 Cov.: 32 AF XY: 0.659 AC XY: 48949 AN XY: 74306

African (AFR) AF: 0.743 AC: 30819 AN: 41490

American (AMR) AF: 0.637 AC: 9719 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2436 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2572 AN: 5168

South Asian (SAS) AF: 0.642 AC: 3093 AN: 4816

European-Finnish (FIN) AF: 0.598 AC: 6306 AN: 10548

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

European-Non Finnish (NFE) AF: 0.635 AC: 43203 AN: 67986

Other (OTH) AF: 0.666 AC: 1410 AN: 2116

Alfa AF: 0.654 Hom.: 5712

Bravo AF: 0.663

Asia WGS AF: 0.559 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	8.8
DANN	Benign	0.91
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs588367; hg19: chr5-16656570;