rs12960119

Positions:

• chr18-26034739-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007559.3(SS18):​c.1096+266T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,046 control chromosomes in the GnomAD database, including 8,624 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 0.25 (8624 hom., cov: 32)
• Consequence: SS18 NM_001007559.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196

Genes affected

SS18 (HGNC:11340): (SS18 subunit of BAF chromatin remodeling complex) Enables nuclear receptor coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of SWI/SNF complex. Implicated in synovial sarcoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SS18	NM_001007559.3	c.1096+266T>C		intron_variant		ENST00000415083.7	NP_001007560.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SS18	ENST00000415083.7	c.1096+266T>C		intron_variant		1	NM_001007559.3	ENSP00000414516	A1

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38629 AN: 151926 Hom.: 8588 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.215

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.255 AC: 38721 AN: 152046 Hom.: 8624 Cov.: 32 AF XY: 0.253 AC XY: 18793 AN XY: 74334

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.0890

Gnomad4 OTH AF: 0.214

Alfa AF: 0.129 Hom.: 1255

Bravo AF: 0.280

Asia WGS AF: 0.232 AC: 804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.73

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

Other links and lift over

dbSNP: rs12960119; hg19: chr18-23614703;