1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006142.5(SFN):​c.*399_*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 0.0087 (4 hom., cov: 0)
  • Exomes 𝑓: 0.0026 (1 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 1254 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFN	NM_006142.5	c.*399_*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.*399_*406dup		3_prime_UTR_variant	1/1		NM_006142.5	P1

Frequencies

GnomAD3 genomes AF: 0.00870 AC: 1253 AN: 144014 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00496

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00619

Gnomad ASJ AF: 0.00322

Gnomad EAS AF: 0.00150

Gnomad SAS AF: 0.00359

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.00463

GnomAD4 exome AF: 0.00260 AC: 152 AN: 58520 Hom.: 1 Cov.: 0 AF XY: 0.00253 AC XY: 75 AN XY: 29676

Gnomad4 AFR exome AF: 0.000927

Gnomad4 AMR exome AF: 0.00145

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000360

Gnomad4 FIN exome AF: 0.00714

Gnomad4 NFE exome AF: 0.00121

Gnomad4 OTH exome AF: 0.000785

GnomAD4 genome AF: 0.00870 AC: 1254 AN: 144096 Hom.: 4 Cov.: 0 AF XY: 0.00831 AC XY: 578 AN XY: 69570

Gnomad4 AFR AF: 0.00495

Gnomad4 AMR AF: 0.00618

Gnomad4 ASJ AF: 0.00322

Gnomad4 EAS AF: 0.00172

Gnomad4 SAS AF: 0.00360

Gnomad4 FIN AF: 0.0103

Gnomad4 NFE AF: 0.0126

Gnomad4 OTH AF: 0.00459

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;