1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGT

Variant summary

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

The NM_006142.5(SFN):​c.*401_*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 0.00617 in 202,256 control chromosomes in the GnomAD database, including 2 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0041 (2 hom., cov: 0)
  • Exomes 𝑓: 0.011 (0 hom.)
• Consequence: SFN NM_006142.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.70

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 596 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFN	NM_006142.5	c.*401_*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.*401_*406del		3_prime_UTR_variant	1/1		NM_006142.5	P1

Frequencies

GnomAD3 genomes AF: 0.00408 AC: 588 AN: 143960 Hom.: 2 Cov.: 0

Gnomad AFR AF: 0.00697

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00250

Gnomad ASJ AF: 0.000585

Gnomad EAS AF: 0.00664

Gnomad SAS AF: 0.00247

Gnomad FIN AF: 0.00163

Gnomad MID AF: 0.00331

Gnomad NFE AF: 0.00317

Gnomad OTH AF: 0.00670

GnomAD4 exome AF: 0.0112 AC: 651 AN: 58216 Hom.: 0 AF XY: 0.0112 AC XY: 332 AN XY: 29522

Gnomad4 AFR exome AF: 0.00139

Gnomad4 AMR exome AF: 0.00632

Gnomad4 ASJ exome AF: 0.00861

Gnomad4 EAS exome AF: 0.00289

Gnomad4 SAS exome AF: 0.00288

Gnomad4 FIN exome AF: 0.0248

Gnomad4 NFE exome AF: 0.00762

Gnomad4 OTH exome AF: 0.00709

GnomAD4 genome AF: 0.00414 AC: 596 AN: 144040 Hom.: 2 Cov.: 0 AF XY: 0.00395 AC XY: 275 AN XY: 69538

Gnomad4 AFR AF: 0.00714

Gnomad4 AMR AF: 0.00250

Gnomad4 ASJ AF: 0.000585

Gnomad4 EAS AF: 0.00666

Gnomad4 SAS AF: 0.00270

Gnomad4 FIN AF: 0.00163

Gnomad4 NFE AF: 0.00317

Gnomad4 OTH AF: 0.00663

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;