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GeneBe

rs17631940

Variant summary

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

The NM_001363830.2(SLFN12L):c.87-10916C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 773,562 control chromosomes in the GnomAD database, including 85,683 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 0.49 ( 18628 hom., cov: 32)
Exomes 𝑓: 0.45 ( 67055 hom. )

Consequence

SLFN12L
NM_001363830.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.53
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]
E2F3P1 (HGNC:3116): (E2F transcription factor 3 pseudogene 1)

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLFN12LNM_001363830.2 linkuse as main transcriptc.87-10916C>T intron_variant ENST00000628453.4
SLFN12LNM_001195790.3 linkuse as main transcriptc.-287-3139C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLFN12LENST00000628453.4 linkuse as main transcriptc.87-10916C>T intron_variant 5 NM_001363830.2 A2
E2F3P1ENST00000589887.1 linkuse as main transcriptn.1103G>A non_coding_transcript_exon_variant 1/1

Frequencies

GnomAD3 genomes
AF:
0.490
AC:
74467
AN:
151898
Hom.:
18625
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.556
Gnomad AMI
AF:
0.470
Gnomad AMR
AF:
0.446
Gnomad ASJ
AF:
0.524
Gnomad EAS
AF:
0.284
Gnomad SAS
AF:
0.300
Gnomad FIN
AF:
0.398
Gnomad MID
AF:
0.503
Gnomad NFE
AF:
0.502
Gnomad OTH
AF:
0.502
GnomAD4 exome
AF:
0.454
AC:
282369
AN:
621548
Hom.:
67055
Cov.:
6
AF XY:
0.449
AC XY:
151683
AN XY:
337526
show subpopulations
Gnomad4 AFR exome
AF:
0.559
Gnomad4 AMR exome
AF:
0.419
Gnomad4 ASJ exome
AF:
0.520
Gnomad4 EAS exome
AF:
0.292
Gnomad4 SAS exome
AF:
0.304
Gnomad4 FIN exome
AF:
0.404
Gnomad4 NFE exome
AF:
0.501
Gnomad4 OTH exome
AF:
0.471
GnomAD4 genome
AF:
0.490
AC:
74500
AN:
152014
Hom.:
18628
Cov.:
32
AF XY:
0.479
AC XY:
35556
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.555
Gnomad4 AMR
AF:
0.446
Gnomad4 ASJ
AF:
0.524
Gnomad4 EAS
AF:
0.284
Gnomad4 SAS
AF:
0.298
Gnomad4 FIN
AF:
0.398
Gnomad4 NFE
AF:
0.502
Gnomad4 OTH
AF:
0.501
Alfa
AF:
0.490
Hom.:
14650
Bravo
AF:
0.501

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
Cadd
Benign
15
Dann
Benign
0.80

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: rs17631940; hg19: chr17-33818130; COSMIC: COSV53470944; COSMIC: COSV53470944; API