chr1-26864330-G-GGT

Variant names:

• chr1-26864330-G-GGT
• rs3065004
• NM_006142.5:c.*405_*406dupTG

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_006142.5(SFN):​c.*405_*406dupTG 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 0.32 (7833 hom., cov: 0)
  • Exomes 𝑓: 0.082 (16 hom.)
• Consequence: SFN NM_006142.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• 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 (EAS) allele frequency at 95% confidence interval = 0.711 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.*405_*406dupTG		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.*405_*406dupTG		3_prime_UTR	Exon 1 of 1	ENSP00000340989.4
	ENSG00000304862	ENST00000806706.1		n.93+711_93+712dupAC		intron	N/A
	ENSG00000304862	ENST00000806707.1		n.80+711_80+712dupAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.323 AC: 46423 AN: 143752 Hom.: 7843 Cov.: 0

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.319

GnomAD4 exome AF: 0.0824 AC: 4797 AN: 58198 Hom.: 16 Cov.: 0 AF XY: 0.0782 AC XY: 2311 AN XY: 29534

African (AFR) AF: 0.0186 AC: 40 AN: 2150

American (AMR) AF: 0.0514 AC: 106 AN: 2062

Ashkenazi Jewish (ASJ) AF: 0.0336 AC: 39 AN: 1162

East Asian (EAS) AF: 0.0372 AC: 77 AN: 2072

South Asian (SAS) AF: 0.0206 AC: 114 AN: 5546

European-Finnish (FIN) AF: 0.224 AC: 3384 AN: 15136

Middle Eastern (MID) AF: 0.0219 AC: 5 AN: 228

European-Non Finnish (NFE) AF: 0.0340 AC: 929 AN: 27304

Other (OTH) AF: 0.0406 AC: 103 AN: 2538

GnomAD4 genome AF: 0.323 AC: 46422 AN: 143836 Hom.: 7833 Cov.: 0 AF XY: 0.330 AC XY: 22924 AN XY: 69422

African (AFR) AF: 0.239 AC: 9270 AN: 38752

American (AMR) AF: 0.430 AC: 6173 AN: 14372

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1001 AN: 3412

East Asian (EAS) AF: 0.731 AC: 3401 AN: 4650

South Asian (SAS) AF: 0.431 AC: 1906 AN: 4420

European-Finnish (FIN) AF: 0.346 AC: 3181 AN: 9204

Middle Eastern (MID) AF: 0.205 AC: 57 AN: 278

European-Non Finnish (NFE) AF: 0.311 AC: 20505 AN: 65932

Other (OTH) AF: 0.322 AC: 629 AN: 1956

Alfa AF: 0.232 Hom.: 273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.022
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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: COSV59433990;