chr15-48646984-A-T

Position:

• chr15-48646984-A-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.1180A>T 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 0.277 in 152,140 control chromosomes in the GnomAD database, including 8,314 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 0.28 (8314 hom., cov: 32)
• Consequence: FBN1-DT NR_183871.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

FBN1-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBN1-DT	NR_183871.1	n.1180A>T		non_coding_transcript_exon_variant	1/2
FBN1-DT	NR_183872.1	n.1026+154A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBN1-DT	ENST00000558061.1	n.880+154A>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42071 AN: 152022 Hom.: 8299 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.0640

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.277 AC: 42126 AN: 152140 Hom.: 8314 Cov.: 32 AF XY: 0.276 AC XY: 20513 AN XY: 74386

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.0640

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.222

Alfa AF: 0.0958 Hom.: 149

Bravo AF: 0.290

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6493334; hg19: chr15-48939181;