chr15-32717277-A-T

Variant names:

• chr15-32717277-A-T
• rs1406389
• ENST00000558441.1:n.1731T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 18 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GREM1-AS1	ENST00000558441.1	n.1731T>A		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.273 AC: 6 AN: 22

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.258 AC: 10688 AN: 41496

American (AMR) AF: 0.195 AC: 2977 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3466

East Asian (EAS) AF: 0.684 AC: 3538 AN: 5176

South Asian (SAS) AF: 0.339 AC: 1633 AN: 4818

European-Finnish (FIN) AF: 0.300 AC: 3177 AN: 10576

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13766 AN: 67952

Other (OTH) AF: 0.239 AC: 505 AN: 2112

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs1406389; hg19: chr15-33009478;