rs6587852

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000647858.1(FGGY-DT):​n.1954+50419T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,030 control chromosomes in the GnomAD database, including 41,398 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 0.74 ( 41398 hom., cov: 32)

Consequence

FGGY-DT
ENST00000647858.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.779
Variant links:
Genes affected
FGGY-DT (HGNC:55265): (FGGY divergent transcript)
LINC01358 (HGNC:50589): (long intergenic non-protein coding RNA 1358)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FGGY-DTENST00000647858.1 linkuse as main transcriptn.1954+50419T>G intron_variant, non_coding_transcript_variant
LINC01358ENST00000625548.1 linkuse as main transcriptn.627-533A>C intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.736
AC:
111840
AN:
151912
Hom.:
41358
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.678
Gnomad AMI
AF:
0.718
Gnomad AMR
AF:
0.801
Gnomad ASJ
AF:
0.644
Gnomad EAS
AF:
0.870
Gnomad SAS
AF:
0.795
Gnomad FIN
AF:
0.801
Gnomad MID
AF:
0.633
Gnomad NFE
AF:
0.739
Gnomad OTH
AF:
0.724
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.736
AC:
111933
AN:
152030
Hom.:
41398
Cov.:
32
AF XY:
0.741
AC XY:
55051
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.678
Gnomad4 AMR
AF:
0.802
Gnomad4 ASJ
AF:
0.644
Gnomad4 EAS
AF:
0.870
Gnomad4 SAS
AF:
0.795
Gnomad4 FIN
AF:
0.801
Gnomad4 NFE
AF:
0.739
Gnomad4 OTH
AF:
0.725
Alfa
AF:
0.736
Hom.:
39638
Bravo
AF:
0.734
Asia WGS
AF:
0.851
AC:
2959
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.2
DANN
Benign
0.66

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs6587852; hg19: chr1-59705447; API