rs257174

Positions:

• chr5-16628402-T-C
• chr5-16628402-T-G

Variant summary

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

The NR_109946.1(RETREG1-AS1):​n.1159-1052T>C variant causes a intron, non coding transcript 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 NR_109946.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.95).
• 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/exons	MANE	Protein	UniProt
RETREG1-AS1	NR_109946.1	n.1159-1052T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RETREG1-AS1	ENST00000653650.1	n.329+11916T>C		intron_variant, non_coding_transcript_variant
RETREG1-AS1	ENST00000499131.1	n.1159-1052T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.348

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.273

Alfa AF: 0.274 Hom.: 11787

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs257174; hg19: chr5-16628511;