rs876095

Variant names:

• chr5-16656694-A-G
• rs876095
• ENST00000653650.1:n.330-22140A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-16656694-A-G
• chr5-16656694-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000653650.1(RETREG1-AS1):​n.330-22140A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.658 in 152,062 control chromosomes in the GnomAD database, including 33,043 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 (33043 hom., cov: 32)
• Consequence: RETREG1-AS1 ENST00000653650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.841

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 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.330-22140A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99926 AN: 151944 Hom.: 32993 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.658 AC: 100030 AN: 152062 Hom.: 33043 Cov.: 32 AF XY: 0.657 AC XY: 48829 AN XY: 74322

Gnomad4 AFR AF: 0.735

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.636

Gnomad4 OTH AF: 0.666

Alfa AF: 0.642 Hom.: 14472

Bravo AF: 0.661

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs876095; hg19: chr5-16656803;