rs2289136

Positions:

• chr15-48652075-G-A
• chr15-48652075-G-C
• chr15-48652075-G-T

Variant summary

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

The NR_183871.1(FBN1-DT):​n.2394G>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 0.812 in 152,114 control chromosomes in the GnomAD database, including 50,331 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 0.81 (50331 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: FBN1-DT NR_183871.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

FBN1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.839 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBN1-DT	NR_183871.1	n.2394G>A		non_coding_transcript_exon_variant	2/2
FBN1-DT	NR_183872.1	n.2148G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123467 AN: 151996 Hom.: 50308 Cov.: 32

Gnomad AFR AF: 0.731

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.872

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.805

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.812 AC: 123534 AN: 152114 Hom.: 50331 Cov.: 32 AF XY: 0.815 AC XY: 60620 AN XY: 74362

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.872

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.798

Alfa AF: 0.835 Hom.: 24180

Bravo AF: 0.807

Asia WGS AF: 0.789 AC: 2744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2289136; hg19: chr15-48944272;