1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGT

Variant summary

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

The NM_006142.5(SFN):​c.*403_*406delTGTG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 202,350 control chromosomes in the GnomAD database, including 3,001 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (2900 hom., cov: 0)
  • Exomes 𝑓: 0.080 (101 hom.)
• Consequence: SFN NM_006142.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

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 (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFN	NM_006142.5	c.*403_*406delTGTG		3_prime_UTR_variant	1/1	ENST00000339276.6	NP_006133.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFN	ENST00000339276.6	c.*403_*406delTGTG		3_prime_UTR_variant	1/1	6	NM_006142.5	ENSP00000340989.4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 26854 AN: 143920 Hom.: 2903 Cov.: 0

Gnomad AFR AF: 0.0594

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.0557

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.197

GnomAD4 exome AF: 0.0795 AC: 4640 AN: 58348 Hom.: 101 AF XY: 0.0777 AC XY: 2299 AN XY: 29576

Gnomad4 AFR exome AF: 0.00557

Gnomad4 AMR exome AF: 0.0355

Gnomad4 ASJ exome AF: 0.0524

Gnomad4 EAS exome AF: 0.00531

Gnomad4 SAS exome AF: 0.0169

Gnomad4 FIN exome AF: 0.208

Gnomad4 NFE exome AF: 0.0395

Gnomad4 OTH exome AF: 0.0463

GnomAD4 genome AF: 0.187 AC: 26857 AN: 144002 Hom.: 2900 Cov.: 0 AF XY: 0.187 AC XY: 13018 AN XY: 69522

Gnomad4 AFR AF: 0.0594

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.0561

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.196

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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;