chr18-26034739-A-G

Variant names:

• chr18-26034739-A-G
• rs12960119
• NM_001007559.3:c.1096+266T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007559.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SS18	NM_001007559.3	MANE Select	c.1096+266T>C		intron	N/A	NP_001007560.1
	SS18	NM_001308201.2		c.1027+266T>C		intron	N/A	NP_001295130.1
	SS18	NM_005637.4		c.1003+266T>C		intron	N/A	NP_005628.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SS18	ENST00000415083.7	TSL:1 MANE Select	c.1096+266T>C		intron	N/A	ENSP00000414516.2
	SS18	ENST00000269137.11	TSL:1	c.1003+266T>C		intron	N/A	ENSP00000269137.7
	SS18	ENST00000582092.1	TSL:1	n.61+266T>C		intron	N/A

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

African (AFR) AF: 0.598 AC: 24750 AN: 41420

American (AMR) AF: 0.234 AC: 3571 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1414 AN: 5166

South Asian (SAS) AF: 0.109 AC: 524 AN: 4826

European-Finnish (FIN) AF: 0.136 AC: 1443 AN: 10586

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0890 AC: 6053 AN: 67980

Other (OTH) AF: 0.214 AC: 453 AN: 2114

Alfa AF: 0.211 Hom.: 5224

Bravo AF: 0.280

Asia WGS AF: 0.232 AC: 804 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.0
DANN	Benign	0.73
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12960119; hg19: chr18-23614703;