5-16628402-T-C

Variant names:

• chr5-16628402-T-C
• rs257174
• ENST00000499131.1:n.1159-1052T>C

Variant summary

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

The ENST00000499131.1(RETREG1-AS1):​n.1159-1052T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 150,902 control chromosomes in the GnomAD database, including 7,135 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 0.30 (7135 hom., cov: 32)
• Consequence: RETREG1-AS1 ENST00000499131.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 7 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RETREG1-AS1	NR_109946.1	n.1159-1052T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RETREG1-AS1	ENST00000499131.1	n.1159-1052T>C		intron_variant	Intron 3 of 3	2
RETREG1-AS1	ENST00000653650.1	n.329+11916T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45691 AN: 150784 Hom.: 7125 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.165

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.303 AC: 45726 AN: 150902 Hom.: 7135 Cov.: 32 AF XY: 0.302 AC XY: 22240 AN XY: 73662

African (AFR) AF: 0.348 AC: 14423 AN: 41414

American (AMR) AF: 0.341 AC: 5190 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 865 AN: 3464

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1492 AN: 4818

European-Finnish (FIN) AF: 0.269 AC: 2722 AN: 10118

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.283 AC: 19054 AN: 67416

Other (OTH) AF: 0.273 AC: 574 AN: 2100

Alfa AF: 0.282 Hom.: 25767

Bravo AF: 0.302

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.16
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs257174; hg19: chr5-16628511;