GeneBe

17-35513276-C-G

Variant names:

Variant summary

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

The NM_001363830.2(SLFN12L):​c.86+9003G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,138 control chromosomes in the GnomAD database, including 49,198 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 0.80 ( 49198 hom., cov: 32)

Consequence

SLFN12L
NM_001363830.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.14

Publications

4 publications found
Variant links:
Genes affected
SLFN12L (HGNC:33920): (schlafen family member 12 like) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-1.03).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLFN12LNM_001363830.2 linkc.86+9003G>C intron_variant Intron 2 of 4 ENST00000628453.4 NP_001350759.2
SLFN12LNM_001195790.3 linkc.-288+9003G>C intron_variant Intron 2 of 5 NP_001182719.2 Q6IEE8

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLFN12LENST00000628453.4 linkc.86+9003G>C intron_variant Intron 2 of 4 5 NM_001363830.2 ENSP00000487397.4 A0A8I5QCZ1

Frequencies

GnomAD3 genomes
AF:
0.803
AC:
122063
AN:
152018
Hom.:
49167
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.802
Gnomad AMI
AF:
0.897
Gnomad AMR
AF:
0.828
Gnomad ASJ
AF:
0.680
Gnomad EAS
AF:
0.779
Gnomad SAS
AF:
0.801
Gnomad FIN
AF:
0.854
Gnomad MID
AF:
0.745
Gnomad NFE
AF:
0.798
Gnomad OTH
AF:
0.781
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.803
AC:
122150
AN:
152138
Hom.:
49198
Cov.:
32
AF XY:
0.805
AC XY:
59850
AN XY:
74370
show subpopulations
African (AFR)
AF:
0.802
AC:
33261
AN:
41480
American (AMR)
AF:
0.828
AC:
12674
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
0.680
AC:
2359
AN:
3470
East Asian (EAS)
AF:
0.779
AC:
4027
AN:
5172
South Asian (SAS)
AF:
0.800
AC:
3855
AN:
4816
European-Finnish (FIN)
AF:
0.854
AC:
9015
AN:
10558
Middle Eastern (MID)
AF:
0.731
AC:
215
AN:
294
European-Non Finnish (NFE)
AF:
0.798
AC:
54269
AN:
68022
Other (OTH)
AF:
0.785
AC:
1657
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1223
2447
3670
4894
6117
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
874
1748
2622
3496
4370
<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:
0.779
Hom.:
2474
Bravo
AF:
0.800
Asia WGS
AF:
0.828
AC:
2877
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
2.2
DANN
Benign
0.20
PhyloP100
-1.1
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs8068353; hg19: chr17-33840295; API