1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGT

Variant names:

• chr1-26864330-GGTGT-G
• rs3065004
• NM_006142.5:c.*403_*406delTGTG

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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]

ENSG00000304862 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006142.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFN	NM_006142.5	MANE Select	c.*403_*406delTGTG		3_prime_UTR	Exon 1 of 1	NP_006133.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFN	ENST00000339276.6	TSL:6 MANE Select	c.*403_*406delTGTG		3_prime_UTR	Exon 1 of 1	ENSP00000340989.4
	ENSG00000304862	ENST00000806706.1		n.93+709_93+712delACAC		intron	N/A
	ENSG00000304862	ENST00000806707.1		n.80+709_80+712delACAC		intron	N/A

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

African (AFR) AF: 0.00557 AC: 12 AN: 2156

American (AMR) AF: 0.0355 AC: 73 AN: 2056

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 61 AN: 1164

East Asian (EAS) AF: 0.00531 AC: 11 AN: 2072

South Asian (SAS) AF: 0.0169 AC: 94 AN: 5550

European-Finnish (FIN) AF: 0.208 AC: 3179 AN: 15282

Middle Eastern (MID) AF: 0.0570 AC: 13 AN: 228

European-Non Finnish (NFE) AF: 0.0395 AC: 1079 AN: 27294

Other (OTH) AF: 0.0463 AC: 118 AN: 2546

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

African (AFR) AF: 0.0594 AC: 2304 AN: 38798

American (AMR) AF: 0.129 AC: 1857 AN: 14396

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1078 AN: 3412

East Asian (EAS) AF: 0.0561 AC: 261 AN: 4650

South Asian (SAS) AF: 0.268 AC: 1191 AN: 4442

European-Finnish (FIN) AF: 0.280 AC: 2590 AN: 9236

Middle Eastern (MID) AF: 0.299 AC: 83 AN: 278

European-Non Finnish (NFE) AF: 0.256 AC: 16860 AN: 65972

Other (OTH) AF: 0.196 AC: 385 AN: 1960

Alfa AF: 0.215 Hom.: 273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3065004; hg19: chr1-27190821; COSMIC: COSV59432894;