1-86862625-C-T

Variant summary

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

The NM_004261.5(SELENOF):​c.*849G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,958 control chromosomes in the GnomAD database, including 6,290 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 0.26 ( 6290 hom., cov: 33)
Failed GnomAD Quality Control

Consequence

SELENOF
NM_004261.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.45
Variant links:
Genes affected
SELENOF (HGNC:17705): (selenoprotein F) The protein encoded by this gene belongs to the SEP15/selenoprotein M family. The exact function of this protein is not known; however, it has been found to associate with UDP-glucose:glycoprotein glucosyltransferase (UGTR), an endoplasmic reticulum(ER)-resident protein, which is involved in the quality control of protein folding. The association with UGTR retains this protein in the ER, where it may play a role in protein folding. It has also been suggested to have a role in cancer etiology. This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Nov 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SELENOFNM_004261.5 linkuse as main transcriptc.*849G>A 3_prime_UTR_variant 5/5 ENST00000331835.10 NP_004252.2 O60613-1
SELENOFNM_203341.3 linkuse as main transcriptc.*922G>A 3_prime_UTR_variant 4/4 NP_976086.1 O60613-2
SELENOFNR_144512.1 linkuse as main transcriptn.1424G>A non_coding_transcript_exon_variant 5/5
SELENOFNR_144513.1 linkuse as main transcriptn.1408G>A non_coding_transcript_exon_variant 5/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SELENOFENST00000331835.10 linkuse as main transcriptc.*849G>A 3_prime_UTR_variant 5/51 NM_004261.5 ENSP00000328729.6 O60613-1

Frequencies

GnomAD3 genomes
AF:
0.259
AC:
39311
AN:
151840
Hom.:
6268
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.446
Gnomad AMI
AF:
0.177
Gnomad AMR
AF:
0.180
Gnomad ASJ
AF:
0.179
Gnomad EAS
AF:
0.0312
Gnomad SAS
AF:
0.170
Gnomad FIN
AF:
0.158
Gnomad MID
AF:
0.218
Gnomad NFE
AF:
0.208
Gnomad OTH
AF:
0.232
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AC:
0
AN:
0
Hom.:
0
Cov.:
0
AC XY:
0
AN XY:
0
GnomAD4 genome
AF:
0.259
AC:
39389
AN:
151958
Hom.:
6290
Cov.:
33
AF XY:
0.252
AC XY:
18741
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.447
Gnomad4 AMR
AF:
0.181
Gnomad4 ASJ
AF:
0.179
Gnomad4 EAS
AF:
0.0315
Gnomad4 SAS
AF:
0.170
Gnomad4 FIN
AF:
0.158
Gnomad4 NFE
AF:
0.208
Gnomad4 OTH
AF:
0.233
Alfa
AF:
0.213
Hom.:
4563
Bravo
AF:
0.265
Asia WGS
AF:
0.164
AC:
567
AN:
3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.10
DANN
Benign
0.29

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs540049; hg19: chr1-87328308; API