15-97539048-T-C

Variant names:

• chr15-97539048-T-C
• rs12912857
• ENST00000625039.1:n.2429A>G

Variant summary

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

The ENST00000625039.1(ENSG00000279091):​n.2429A>G 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 0.708 in 152,098 control chromosomes in the GnomAD database, including 38,738 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 0.71 (38715 hom., cov: 31)
  • Exomes 𝑓: 0.68 (23 hom.)
• Consequence: ENSG00000279091 ENST00000625039.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

Genes affected

ENSG00000279091 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 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
ENSG00000279091	ENST00000625039.1	n.2429A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107573 AN: 151874 Hom.: 38665 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.700

GnomAD4 exome AF: 0.679 AC: 72 AN: 106 Hom.: 23 Cov.: 0 AF XY: 0.700 AC XY: 63 AN XY: 90

Gnomad4 AFR exome AF: 1.00

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 NFE exome AF: 0.659

Gnomad4 OTH exome AF: 0.750

GnomAD4 genome AF: 0.708 AC: 107684 AN: 151992 Hom.: 38715 Cov.: 31 AF XY: 0.717 AC XY: 53289 AN XY: 74282

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.727

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.765

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.703

Alfa AF: 0.679 Hom.: 6301

Bravo AF: 0.715

Asia WGS AF: 0.813 AC: 2829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.17
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12912857; hg19: chr15-98082278;