ENST00000558441.1:n.1635G>C

Variant names:

• chr15-32717373-C-G
• rs1919364
• ENST00000558441.1:n.1635G>C

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GREM1-AS1	ENST00000558441.1	n.1635G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;