20-62159842-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_198935.3(SS18L1):​c.147-35G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00928 in 1,602,256 control chromosomes in the GnomAD database, including 663 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.037 ( 332 hom., cov: 30)
Exomes 𝑓: 0.0063 ( 331 hom. )

Consequence

SS18L1
NM_198935.3 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.666
Variant links:
Genes affected
SS18L1 (HGNC:15592): (SS18L1 subunit of BAF chromatin remodeling complex) This gene encodes a calcium-responsive transactivator which is an essential subunit of a neuron-specific chromatin-remodeling complex. The structure of this gene is similar to that of the SS18 gene. Mutations in this gene are involved in amyotrophic lateral sclerosis (ALS). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 20-62159842-G-A is Benign according to our data. Variant chr20-62159842-G-A is described in ClinVar as [Benign]. Clinvar id is 1262811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SS18L1NM_198935.3 linkuse as main transcriptc.147-35G>A intron_variant ENST00000331758.8 NP_945173.1 O75177-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SS18L1ENST00000331758.8 linkuse as main transcriptc.147-35G>A intron_variant 1 NM_198935.3 ENSP00000333012.3 O75177-1
SS18L1ENST00000450482.5 linkuse as main transcriptc.156-35G>A intron_variant 5 ENSP00000398634.1 Q9BR54

Frequencies

GnomAD3 genomes
AF:
0.0373
AC:
5664
AN:
151962
Hom.:
330
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.124
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0145
Gnomad ASJ
AF:
0.0107
Gnomad EAS
AF:
0.000388
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00151
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00321
Gnomad OTH
AF:
0.0263
GnomAD3 exomes
AF:
0.0118
AC:
2820
AN:
239514
Hom.:
141
AF XY:
0.00937
AC XY:
1217
AN XY:
129914
show subpopulations
Gnomad AFR exome
AF:
0.125
Gnomad AMR exome
AF:
0.00883
Gnomad ASJ exome
AF:
0.0131
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000544
Gnomad FIN exome
AF:
0.00122
Gnomad NFE exome
AF:
0.00353
Gnomad OTH exome
AF:
0.00830
GnomAD4 exome
AF:
0.00633
AC:
9182
AN:
1450176
Hom.:
331
Cov.:
29
AF XY:
0.00582
AC XY:
4200
AN XY:
721224
show subpopulations
Gnomad4 AFR exome
AF:
0.134
Gnomad4 AMR exome
AF:
0.00921
Gnomad4 ASJ exome
AF:
0.0131
Gnomad4 EAS exome
AF:
0.0000508
Gnomad4 SAS exome
AF:
0.000634
Gnomad4 FIN exome
AF:
0.00133
Gnomad4 NFE exome
AF:
0.00269
Gnomad4 OTH exome
AF:
0.0130
GnomAD4 genome
AF:
0.0373
AC:
5680
AN:
152080
Hom.:
332
Cov.:
30
AF XY:
0.0367
AC XY:
2726
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.0145
Gnomad4 ASJ
AF:
0.0107
Gnomad4 EAS
AF:
0.000389
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00151
Gnomad4 NFE
AF:
0.00321
Gnomad4 OTH
AF:
0.0260
Alfa
AF:
0.0201
Hom.:
30
Bravo
AF:
0.0425
Asia WGS
AF:
0.00664
AC:
23
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxMay 21, 2021- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.7
DANN
Benign
0.51
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.2

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

LitVar

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

Other links and lift over

dbSNP: rs77569924; hg19: chr20-60734898; API