17-35519585-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001363830.2(SLFN12L):​c.86+2694C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,982 control chromosomes in the GnomAD database, including 33,516 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 0.65 ( 33516 hom., cov: 31)

Consequence

SLFN12L
NM_001363830.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.252
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 made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SLFN12LNM_001363830.2 linkuse as main transcriptc.86+2694C>T intron_variant ENST00000628453.4 NP_001350759.2
SLFN12LNM_001195790.3 linkuse as main transcriptc.-288+2694C>T intron_variant NP_001182719.2 Q6IEE8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SLFN12LENST00000628453.4 linkuse as main transcriptc.86+2694C>T intron_variant 5 NM_001363830.2 ENSP00000487397.4 A0A8I5QCZ1

Frequencies

GnomAD3 genomes
AF:
0.647
AC:
98201
AN:
151862
Hom.:
33521
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.421
Gnomad AMI
AF:
0.895
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.618
Gnomad EAS
AF:
0.547
Gnomad SAS
AF:
0.614
Gnomad FIN
AF:
0.790
Gnomad MID
AF:
0.544
Gnomad NFE
AF:
0.748
Gnomad OTH
AF:
0.659
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.646
AC:
98217
AN:
151982
Hom.:
33516
Cov.:
31
AF XY:
0.648
AC XY:
48141
AN XY:
74278
show subpopulations
Gnomad4 AFR
AF:
0.420
Gnomad4 AMR
AF:
0.741
Gnomad4 ASJ
AF:
0.618
Gnomad4 EAS
AF:
0.546
Gnomad4 SAS
AF:
0.614
Gnomad4 FIN
AF:
0.790
Gnomad4 NFE
AF:
0.748
Gnomad4 OTH
AF:
0.659
Alfa
AF:
0.722
Hom.:
79471
Bravo
AF:
0.634
Asia WGS
AF:
0.570
AC:
1981
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.2
DANN
Benign
0.65

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4796093; hg19: chr17-33846604; API