NM_001007559.3:c.147-1075G>A

Variant names:

• chr18-26079235-C-T
• rs9304489
• NM_001007559.3:c.147-1075G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007559.3(SS18):​c.147-1075G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,130 control chromosomes in the GnomAD database, including 5,784 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 0.19 (5784 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SS18 NM_001007559.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.491 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.147-1075G>A		intron	N/A	NP_001007560.1
	SS18	NM_001308201.2		c.78-1075G>A		intron	N/A	NP_001295130.1
	SS18	NM_005637.4		c.147-1075G>A		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.147-1075G>A		intron	N/A	ENSP00000414516.2
	SS18	ENST00000269137.11	TSL:1	c.147-1075G>A		intron	N/A	ENSP00000269137.7
	SS18	ENST00000539244.6	TSL:1	n.70-1075G>A		intron	N/A	ENSP00000441760.2

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29190 AN: 152012 Hom.: 5768 Cov.: 33

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0941

Gnomad FIN AF: 0.0655

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0461

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.192 AC: 29255 AN: 152130 Hom.: 5784 Cov.: 33 AF XY: 0.189 AC XY: 14067 AN XY: 74384

African (AFR) AF: 0.497 AC: 20597 AN: 41438

American (AMR) AF: 0.198 AC: 3022 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0559 AC: 194 AN: 3470

East Asian (EAS) AF: 0.149 AC: 772 AN: 5178

South Asian (SAS) AF: 0.0937 AC: 452 AN: 4822

European-Finnish (FIN) AF: 0.0655 AC: 695 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0461 AC: 3134 AN: 67996

Other (OTH) AF: 0.165 AC: 350 AN: 2116

Alfa AF: 0.148 Hom.: 707

Bravo AF: 0.220

Asia WGS AF: 0.160 AC: 556 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.73
PhyloP100		0.0060
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: rs9304489; hg19: chr18-23659199;