1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGT

Variant summary

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

The NM_006142.5(SFN):​c.*403_*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 0.064 (302 hom., cov: 0)
  • Exomes 𝑓: 0.018 (4 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 (AFR) allele frequency at 95% confidence interval = 0.0739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFN	NM_006142.5	c.*403_*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.*403_*406dup		3_prime_UTR_variant	1/1		NM_006142.5	P1

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9216 AN: 143916 Hom.: 302 Cov.: 0

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.0279

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.0700

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0568

GnomAD4 exome AF: 0.0177 AC: 1036 AN: 58430 Hom.: 4 Cov.: 0 AF XY: 0.0175 AC XY: 517 AN XY: 29624

Gnomad4 AFR exome AF: 0.00279

Gnomad4 AMR exome AF: 0.00485

Gnomad4 ASJ exome AF: 0.00515

Gnomad4 EAS exome AF: 0.00241

Gnomad4 SAS exome AF: 0.00270

Gnomad4 FIN exome AF: 0.0511

Gnomad4 NFE exome AF: 0.00721

Gnomad4 OTH exome AF: 0.00471

GnomAD4 genome AF: 0.0640 AC: 9222 AN: 143998 Hom.: 302 Cov.: 0 AF XY: 0.0647 AC XY: 4501 AN XY: 69516

Gnomad4 AFR AF: 0.0762

Gnomad4 AMR AF: 0.0523

Gnomad4 ASJ AF: 0.0536

Gnomad4 EAS AF: 0.0411

Gnomad4 SAS AF: 0.0576

Gnomad4 FIN AF: 0.0893

Gnomad4 NFE AF: 0.0592

Gnomad4 OTH AF: 0.0562

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;