dbSNP rs1055636: SLFN5:c.*1413A>C (chr17-35267301-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_144975.4(SLFN5):c.*1413A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,118 control chromosomes in the GnomAD database, including 10,021 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 0.33 ( 10021 hom., cov: 32)

Exomes 𝑓: 0.25 ( 0 hom. )

Consequence

SLFN5
NM_144975.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0700

Publications

16 publications found

Variant links:

Genes affected

SLFN5 (HGNC:28286): (schlafen family member 5) Predicted to enable ATP binding activity. Predicted to be involved in cell differentiation. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

SLFN5 links:

Genome browser will be placed here

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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144975.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLFN5	NM_144975.4	MANE Select	c.*1413A>C		3_prime_UTR	Exon 5 of 5	NP_659412.3
	SLFN5	NM_001330183.2		c.*2198A>C		3_prime_UTR	Exon 4 of 4	NP_001317112.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SLFN5	ENST00000299977.9	TSL:1 MANE Select	c.*1413A>C	3_prime_UTR	Exon 5 of 5	ENSP00000299977.3
SLFN5	ENST00000884250.1		c.*1413A>C	3_prime_UTR	Exon 5 of 5	ENSP00000554309.1
SLFN5	ENST00000884251.1		c.*1413A>C	3_prime_UTR	Exon 5 of 5	ENSP00000554310.1

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49795

AN:

151996

Hom.:

10025

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.267

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.535

Gnomad EAS

AF:

0.0897

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.427

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.453

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.250

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.625

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.327

AC:

49786

AN:

152114

Hom.:

10021

Cov.:

AF XY:

0.323

AC XY:

24021

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.120

AC:

4983

AN:

41542

American (AMR)

AF:

0.307

AC:

4692

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.535

AC:

1856

AN:

3468

East Asian (EAS)

AF:

0.0897

AC:

465

AN:

5182

South Asian (SAS)

AF:

0.281

AC:

1357

AN:

4828

European-Finnish (FIN)

AF:

0.427

AC:

4503

AN:

10548

Middle Eastern (MID)

AF:

0.510

AC:

149

AN:

292

European-Non Finnish (NFE)

AF:

0.453

AC:

30775

AN:

67966

Other (OTH)

AF:

0.362

AC:

763

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1552

3105

4657

6210

7762

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.408

Hom.:

38263

Bravo

AF:

0.308

Asia WGS

AF:

0.190

AC:

662

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

3.9

(source)

DANN

Benign

0.88

PhyloP100

-0.070

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