chr1-26864330-G-GGTGT

Variant names:

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

Variant summary

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

The NM_006142.5(SFN):​c.*403_*406dupTGTG 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 0.064 (302 hom., cov: 0)
  • Exomes 𝑓: 0.018 (4 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 (AFR) allele frequency at 95% confidence interval = 0.0739 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_*406dupTGTG		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_*406dupTGTG		3_prime_UTR	Exon 1 of 1	ENSP00000340989.4
	ENSG00000304862	ENST00000806706.1		n.93+709_93+712dupACAC		intron	N/A
	ENSG00000304862	ENST00000806707.1		n.80+709_80+712dupACAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0640 AC: 9216 AN: 143916 Hom.: 302 Cov.: 0

Gnomad AFR AF: 0.0762

Gnomad AMI AF: 0.0279

Gnomad AMR AF: 0.0525

Gnomad ASJ AF: 0.0536

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.0700

Gnomad NFE AF: 0.0592

Gnomad OTH AF: 0.0568

GnomAD4 exome AF: 0.0177 AC: 1036 AN: 58430 Hom.: 4 Cov.: 0 AF XY: 0.0175 AC XY: 517 AN XY: 29624

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00279 AC: 6 AN: 2154

American (AMR) AF: 0.00485 AC: 10 AN: 2062

Ashkenazi Jewish (ASJ) AF: 0.00515 AC: 6 AN: 1164

East Asian (EAS) AF: 0.00241 AC: 5 AN: 2074

South Asian (SAS) AF: 0.00270 AC: 15 AN: 5554

European-Finnish (FIN) AF: 0.0511 AC: 784 AN: 15334

Middle Eastern (MID) AF: 0.00439 AC: 1 AN: 228

European-Non Finnish (NFE) AF: 0.00721 AC: 197 AN: 27312

Other (OTH) AF: 0.00471 AC: 12 AN: 2548

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.0640 AC: 9222 AN: 143998 Hom.: 302 Cov.: 0 AF XY: 0.0647 AC XY: 4501 AN XY: 69516

African (AFR) AF: 0.0762 AC: 2955 AN: 38780

American (AMR) AF: 0.0523 AC: 753 AN: 14390

Ashkenazi Jewish (ASJ) AF: 0.0536 AC: 183 AN: 3416

East Asian (EAS) AF: 0.0411 AC: 191 AN: 4650

South Asian (SAS) AF: 0.0576 AC: 256 AN: 4442

European-Finnish (FIN) AF: 0.0893 AC: 824 AN: 9230

Middle Eastern (MID) AF: 0.0725 AC: 20 AN: 276

European-Non Finnish (NFE) AF: 0.0592 AC: 3906 AN: 65996

Other (OTH) AF: 0.0562 AC: 110 AN: 1958

Alfa AF: 0.0441 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;