1-86906079-C-T

Variant names:

• chr1-86906079-C-T
• rs561104
• NM_004261.5:c.85-2631G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004261.5(SELENOF):​c.85-2631G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.641 in 152,054 control chromosomes in the GnomAD database, including 32,265 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 0.64 (32265 hom., cov: 32)
• Consequence: SELENOF NM_004261.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362
• Publications: 14 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SELENOF	NM_004261.5	c.85-2631G>A		intron_variant	Intron 1 of 4	ENST00000331835.10	NP_004252.2
SELENOF	NM_203341.3	c.85-2631G>A		intron_variant	Intron 1 of 3		NP_976086.1
SELENOF	NR_144512.1	n.162-2631G>A		intron_variant	Intron 1 of 4
SELENOF	NR_144513.1	n.146-2631G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SELENOF	ENST00000331835.10	c.85-2631G>A		intron_variant	Intron 1 of 4	1	NM_004261.5	ENSP00000328729.6

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97396 AN: 151936 Hom.: 32211 Cov.: 32

Gnomad AFR AF: 0.817

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.481

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.641 AC: 97517 AN: 152054 Hom.: 32265 Cov.: 32 AF XY: 0.638 AC XY: 47367 AN XY: 74294

African (AFR) AF: 0.818 AC: 33946 AN: 41512

American (AMR) AF: 0.579 AC: 8847 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2496 AN: 5174

South Asian (SAS) AF: 0.650 AC: 3128 AN: 4810

European-Finnish (FIN) AF: 0.536 AC: 5631 AN: 10512

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.575 AC: 39118 AN: 67976

Other (OTH) AF: 0.641 AC: 1357 AN: 2116

Alfa AF: 0.607 Hom.: 80372

Bravo AF: 0.651

Asia WGS AF: 0.591 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.14
DANN	Benign	0.59
PhyloP100		-0.36
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs561104; hg19: chr1-87371762;