1-26864330-GGTGTGTGTGTGTGTGTGT-GGTGTGTGTGTGTGTGTGTGTGTGTGT

Variant names:

• chr1-26864330-G-GGTGTGTGT
• rs3065004
• NM_006142.5:c.*399_*406dupTGTGTGTG

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_006142.5(SFN):​c.*399_*406dupTGTGTGTG 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 0.0087 (4 hom., cov: 0)
  • Exomes 𝑓: 0.0026 (1 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: Likely_benign. The variant received -4 ACMG points.

• BS2: High AC in GnomAd4 at 1254 AD gene.

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.*399_*406dupTGTGTGTG		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.*399_*406dupTGTGTGTG		3_prime_UTR	Exon 1 of 1	ENSP00000340989.4
	ENSG00000304862	ENST00000806706.1		n.93+705_93+712dupACACACAC		intron	N/A
	ENSG00000304862	ENST00000806707.1		n.80+705_80+712dupACACACAC		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00870 AC: 1253 AN: 144014 Hom.: 4 Cov.: 0

Gnomad AFR AF: 0.00496

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00619

Gnomad ASJ AF: 0.00322

Gnomad EAS AF: 0.00150

Gnomad SAS AF: 0.00359

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.00463

GnomAD4 exome AF: 0.00260 AC: 152 AN: 58520 Hom.: 1 Cov.: 0 AF XY: 0.00253 AC XY: 75 AN XY: 29676

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

African (AFR) AF: 0.000927 AC: 2 AN: 2158

American (AMR) AF: 0.00145 AC: 3 AN: 2062

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1164

East Asian (EAS) AF: 0.00 AC: 0 AN: 2074

South Asian (SAS) AF: 0.000360 AC: 2 AN: 5554

European-Finnish (FIN) AF: 0.00714 AC: 110 AN: 15402

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 228

European-Non Finnish (NFE) AF: 0.00121 AC: 33 AN: 27330

Other (OTH) AF: 0.000785 AC: 2 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: 0.00870 AC: 1254 AN: 144096 Hom.: 4 Cov.: 0 AF XY: 0.00831 AC XY: 578 AN XY: 69570

African (AFR) AF: 0.00495 AC: 192 AN: 38816

American (AMR) AF: 0.00618 AC: 89 AN: 14400

Ashkenazi Jewish (ASJ) AF: 0.00322 AC: 11 AN: 3418

East Asian (EAS) AF: 0.00172 AC: 8 AN: 4654

South Asian (SAS) AF: 0.00360 AC: 16 AN: 4442

European-Finnish (FIN) AF: 0.0103 AC: 95 AN: 9240

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 278

European-Non Finnish (NFE) AF: 0.0126 AC: 834 AN: 66026

Other (OTH) AF: 0.00459 AC: 9 AN: 1962

Alfa AF: 0.00667 Hom.: 273

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.022

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;