1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGT

Variant summary

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

The NM_006142.5(SFN):​c.*397_*406del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000676 in 202,566 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00080 (0 hom., cov: 0)
  • Exomes 𝑓: 0.00038 (0 hom.)
• Consequence: SFN NM_006142.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.14

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 115 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFN	NM_006142.5	c.*397_*406del		3_prime_UTR_variant	1/1	ENST00000339276.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFN	ENST00000339276.6	c.*397_*406del		3_prime_UTR_variant	1/1		NM_006142.5	P1

Frequencies

GnomAD3 genomes AF: 0.000798 AC: 115 AN: 144032 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000387

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00139

Gnomad ASJ AF: 0.000293

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000541

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00104

Gnomad OTH AF: 0.00257

GnomAD4 exome AF: 0.000376 AC: 22 AN: 58534 Hom.: 0 AF XY: 0.000438 AC XY: 13 AN XY: 29680

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000970

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000778

Gnomad4 NFE exome AF: 0.000293

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.000798 AC: 115 AN: 144032 Hom.: 0 Cov.: 0 AF XY: 0.000806 AC XY: 56 AN XY: 69478

Gnomad4 AFR AF: 0.000387

Gnomad4 AMR AF: 0.00139

Gnomad4 ASJ AF: 0.000293

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000541

Gnomad4 NFE AF: 0.00104

Gnomad4 OTH AF: 0.00257

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;