1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGT

Position:

• chr1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

The NM_006142.5(SFN):​c.*401_*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 0.0090 (11 hom., cov: 0)
  • Exomes 𝑓: 0.0023 (0 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.

• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00895 (1290/144098) while in subpopulation SAS AF= 0.0194 (86/4438). AF 95% confidence interval is 0.0161. There are 11 homozygotes in gnomad4. There are 615 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 1290 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00899 AC: 1294 AN: 144016 Hom.: 11 Cov.: 0

Gnomad AFR AF: 0.00550

Gnomad AMI AF: 0.00116

Gnomad AMR AF: 0.0108

Gnomad ASJ AF: 0.00176

Gnomad EAS AF: 0.0107

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.00671

Gnomad MID AF: 0.00993

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0118

GnomAD4 exome AF: 0.00232 AC: 136 AN: 58526 Hom.: 0 Cov.: 0 AF XY: 0.00263 AC XY: 78 AN XY: 29670

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00145

Gnomad4 ASJ exome AF: 0.000861

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00108

Gnomad4 FIN exome AF: 0.00532

Gnomad4 NFE exome AF: 0.00154

Gnomad4 OTH exome AF: 0.000392

GnomAD4 genome AF: 0.00895 AC: 1290 AN: 144098 Hom.: 11 Cov.: 0 AF XY: 0.00884 AC XY: 615 AN XY: 69568

Gnomad4 AFR AF: 0.00551

Gnomad4 AMR AF: 0.0107

Gnomad4 ASJ AF: 0.00176

Gnomad4 EAS AF: 0.0103

Gnomad4 SAS AF: 0.0194

Gnomad4 FIN AF: 0.00671

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0117

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;