15-32717373-C-G

Position:

• chr15-32717373-C-G

Variant summary

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

The ENST00000558441.1(GREM1-AS1):​n.1635G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 152,036 control chromosomes in the GnomAD database, including 31,502 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 0.62 (31494 hom., cov: 31)
  • Exomes 𝑓: 0.58 (8 hom.)
• Consequence: GREM1-AS1 ENST00000558441.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406

Genes affected

GREM1-AS1 (HGNC:55411): (GREM1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.936 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GREM1-AS1	ENST00000558441.1	n.1635G>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.625 AC: 94853 AN: 151880 Hom.: 31453 Cov.: 31

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.589

GnomAD4 exome AF: 0.579 AC: 22 AN: 38 Hom.: 8 Cov.: 0 AF XY: 0.577 AC XY: 15 AN XY: 26

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.536

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.625 AC: 94952 AN: 151998 Hom.: 31494 Cov.: 31 AF XY: 0.630 AC XY: 46835 AN XY: 74286

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.494

Gnomad4 OTH AF: 0.591

Alfa AF: 0.553 Hom.: 3059

Bravo AF: 0.630

Asia WGS AF: 0.847 AC: 2942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1919364; hg19: chr15-33009574;