1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_006142.5(SFN):​c.*405_*406dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (7833 hom., cov: 0)
  • Exomes 𝑓: 0.082 (16 hom.)
• Consequence: SFN NM_006142.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220

Genes affected

SFN (HGNC:10773): (stratifin) This gene encodes a cell cycle checkpoint protein. The encoded protein binds to translation and initiation factors and functions as a regulator of mitotic translation. In response to DNA damage this protein plays a role in preventing DNA errors during mitosis. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFN	NM_006142.5	c.*405_*406dup		3_prime_UTR_variant	1/1	ENST00000339276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFN	ENST00000339276.6	c.*405_*406dup		3_prime_UTR_variant	1/1		NM_006142.5	P1

Frequencies

GnomAD3 genomes AF: 0.323 AC: 46423 AN: 143752 Hom.: 7843 Cov.: 0

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.0824 AC: 4797 AN: 58198 Hom.: 16 Cov.: 0 AF XY: 0.0782 AC XY: 2311 AN XY: 29534

Gnomad4 AFR exome AF: 0.0186

Gnomad4 AMR exome AF: 0.0514

Gnomad4 ASJ exome AF: 0.0336

Gnomad4 EAS exome AF: 0.0372

Gnomad4 SAS exome AF: 0.0206

Gnomad4 FIN exome AF: 0.224

Gnomad4 NFE exome AF: 0.0340

Gnomad4 OTH exome AF: 0.0406

GnomAD4 genome AF: 0.323 AC: 46422 AN: 143836 Hom.: 7833 Cov.: 0 AF XY: 0.330 AC XY: 22924 AN XY: 69422

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.322

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3065004; hg19: chr1-27190821;