rs10520842

Positions:

• chr5-16626608-G-T

Variant summary

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

The NR_109946.1(RETREG1-AS1):​n.1158+852G>T 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 0.0797 in 152,108 control chromosomes in the GnomAD database, including 648 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 0.080 (648 hom., cov: 32)
• Consequence: RETREG1-AS1 NR_109946.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RETREG1-AS1	NR_109946.1	n.1158+852G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RETREG1-AS1	ENST00000653650.1	n.329+10122G>T		intron_variant, non_coding_transcript_variant
RETREG1-AS1	ENST00000700847.1	n.905G>T		non_coding_transcript_exon_variant	2/2
RETREG1-AS1	ENST00000499131.1	n.1158+852G>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12118 AN: 151990 Hom.: 647 Cov.: 32

Gnomad AFR AF: 0.0366

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0805

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.100

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.0904

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0797 AC: 12116 AN: 152108 Hom.: 648 Cov.: 32 AF XY: 0.0824 AC XY: 6123 AN XY: 74338

Gnomad4 AFR AF: 0.0365

Gnomad4 AMR AF: 0.0804

Gnomad4 ASJ AF: 0.0588

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0904

Gnomad4 NFE AF: 0.0954

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0917 Hom.: 923

Bravo AF: 0.0722

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520842; hg19: chr5-16626717;