15-32717277-A-T

Position:

• chr15-32717277-A-T

Variant summary

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

The ENST00000558441.1(GREM1-AS1):​n.1731T>A 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 0.243 in 152,104 control chromosomes in the GnomAD database, including 5,191 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 0.24 (5191 hom., cov: 33)
  • Exomes 𝑓: 0.27 (0 hom.)
• Consequence: GREM1-AS1 ENST00000558441.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

GREM1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32717277A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GREM1-AS1	ENST00000558441.1	n.1731T>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36964 AN: 151964 Hom.: 5185 Cov.: 33

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.233

GnomAD4 exome AF: 0.273 AC: 6 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.250 AC XY: 5 AN XY: 20

Gnomad4 NFE exome AF: 0.273

GnomAD4 genome AF: 0.243 AC: 36989 AN: 152082 Hom.: 5191 Cov.: 33 AF XY: 0.249 AC XY: 18509 AN XY: 74364

Gnomad4 AFR AF: 0.258

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.239

Alfa AF: 0.217 Hom.: 501

Bravo AF: 0.237

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1406389; hg19: chr15-33009478;