Genetic Variant SLFN11:c.1070-26G>A (chr17-35360397-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001376007.1(SLFN11):c.1070-26G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,586,064 control chromosomes in the GnomAD database, including 66,354 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.37 ( 12499 hom., cov: 29)

Exomes 𝑓: 0.26 ( 53855 hom. )

Consequence

SLFN11
NM_001376007.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0760

Publications

11 publications found

Variant links:

Genes affected

SLFN11 (HGNC:26633): (schlafen family member 11) Enables tRNA binding activity. Involved in several processes, including defense response to virus; negative regulation of G1/S transition of mitotic cell cycle; and replication fork arrest. Located in cytosol; nucleoplasm; and site of DNA damage. [provided by Alliance of Genome Resources, Apr 2022]

SLFN11 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001376007.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLFN11	NM_001376007.1	MANE Select	c.1070-26G>A	intron	N/A	NP_001362936.1
SLFN11	NM_001104587.2		c.1070-26G>A	intron	N/A	NP_001098057.1
SLFN11	NM_001104588.2		c.1070-26G>A	intron	N/A	NP_001098058.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLFN11	ENST00000685675.1	MANE Select	c.1070-26G>A	intron	N/A	ENSP00000510787.1
SLFN11	ENST00000308377.8	TSL:1	c.1070-26G>A	intron	N/A	ENSP00000312402.4
SLFN11	ENST00000394566.5	TSL:2	c.1070-26G>A	intron	N/A	ENSP00000378067.1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

55595

AN:

150480

Hom.:

12477

Cov.:

show subpopulations

Gnomad AFR

AF:

0.617

Gnomad AMI

AF:

0.392

Gnomad AMR

AF:

0.396

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.480

Gnomad SAS

AF:

0.344

Gnomad FIN

AF:

0.297

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.330

GnomAD2 exomes

AF:

0.320

AC:

74170

AN:

231654

AF XY:

0.306

show subpopulations

Gnomad AFR exome

AF:

0.622

Gnomad AMR exome

AF:

0.455

Gnomad ASJ exome

AF:

0.202

Gnomad EAS exome

AF:

0.494

Gnomad FIN exome

AF:

0.290

Gnomad NFE exome

AF:

0.227

Gnomad OTH exome

AF:

0.286

GnomAD4 exome

AF:

0.258

AC:

370171

AN:

1435464

Hom.:

53855

Cov.:

AF XY:

0.257

AC XY:

183750

AN XY:

713704

show subpopulations

African (AFR)

AF:

0.627

AC:

19848

AN:

31650

American (AMR)

AF:

0.446

AC:

17295

AN:

38780

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

5117

AN:

25236

East Asian (EAS)

AF:

0.492

AC:

19287

AN:

39206

South Asian (SAS)

AF:

0.329

AC:

26819

AN:

81568

European-Finnish (FIN)

AF:

0.289

AC:

15226

AN:

52686

Middle Eastern (MID)

AF:

0.251

AC:

1426

AN:

5692

European-Non Finnish (NFE)

AF:

0.225

AC:

248267

AN:

1101252

Other (OTH)

AF:

0.284

AC:

16886

AN:

59394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

11558

23116

34673

46231

57789

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8926

17852

26778

35704

44630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.370

AC:

55664

AN:

150600

Hom.:

12499

Cov.:

AF XY:

0.374

AC XY:

27445

AN XY:

73438

show subpopulations

African (AFR)

AF:

0.617

AC:

25284

AN:

40994

American (AMR)

AF:

0.396

AC:

5952

AN:

15044

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

749

AN:

3458

East Asian (EAS)

AF:

0.479

AC:

2448

AN:

5106

South Asian (SAS)

AF:

0.343

AC:

1631

AN:

4758

European-Finnish (FIN)

AF:

0.297

AC:

3035

AN:

10216

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.228

AC:

15426

AN:

67732

Other (OTH)

AF:

0.332

AC:

694

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1505

3009

4514

6018

7523

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.272

Hom.:

29314

Bravo

AF:

0.389

Asia WGS

AF:

0.436

AC:

1515

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

2.1

(source)

DANN

Benign

0.75

PhyloP100

-0.076

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over