NR_183871.1:n.2394G>A

Variant names:

• chr15-48652075-G-A
• rs2289136
• NR_183871.1:n.2394G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

FBN1-DT (HGNC:55413): (FBN1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FBN1-DT	NR_183871.1	n.2394G>A		non_coding_transcript_exon_variant	Exon 2 of 2
FBN1-DT	NR_183872.1	n.2148G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN1-DT	ENST00000558061.2	n.*59G>A		downstream_gene_variant		3

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

African (AFR) AF: 0.731 AC: 30271 AN: 41436

American (AMR) AF: 0.830 AC: 12692 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2826 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4418 AN: 5184

South Asian (SAS) AF: 0.833 AC: 4006 AN: 4810

European-Finnish (FIN) AF: 0.872 AC: 9230 AN: 10586

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.845 AC: 57438 AN: 68014

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.835 Hom.: 26873

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
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2289136; hg19: chr15-48944272;