9-136380071-G-A

Variant names:

• chr9-136380071-G-A
• rs11145793
• NM_003086.4:c.2500-207C>T

Variant summary

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

The NM_003086.4(SNAPC4):​c.2500-207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,202 control chromosomes in the GnomAD database, including 3,711 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 0.21 (3711 hom., cov: 33)
• Consequence: SNAPC4 NM_003086.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 21 publications found

Genes affected

SNAPC4 (HGNC:11137): (small nuclear RNA activating complex polypeptide 4) This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]

SNAPC4 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction

  Inheritance: AR Classification: MODERATE Submitted by: Baylor College of Medicine Research Center, G2P

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003086.4. 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
	SNAPC4	NM_003086.4	MANE Select	c.2500-207C>T		intron	N/A	NP_003077.2
	SNAPC4	NM_001394201.1		c.2500-207C>T		intron	N/A	NP_001381130.1
	SNAPC4	NM_001394202.1		c.2416-207C>T		intron	N/A	NP_001381131.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNAPC4	ENST00000684778.1	MANE Select	c.2500-207C>T		intron	N/A	ENSP00000510559.1
	SNAPC4	ENST00000298532.2	TSL:1	c.2500-207C>T		intron	N/A	ENSP00000298532.2
	SNAPC4	ENST00000637388.2	TSL:5	c.2500-207C>T		intron	N/A	ENSP00000490037.2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32029 AN: 152084 Hom.: 3710 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.211 AC: 32045 AN: 152202 Hom.: 3711 Cov.: 33 AF XY: 0.211 AC XY: 15692 AN XY: 74414

African (AFR) AF: 0.133 AC: 5515 AN: 41548

American (AMR) AF: 0.269 AC: 4116 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 720 AN: 3468

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5186

South Asian (SAS) AF: 0.158 AC: 764 AN: 4828

European-Finnish (FIN) AF: 0.278 AC: 2948 AN: 10588

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.250 AC: 16964 AN: 67974

Other (OTH) AF: 0.218 AC: 461 AN: 2112

Alfa AF: 0.226 Hom.: 3638

Bravo AF: 0.203

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	14
DANN	Benign	0.67
PhyloP100		-0.025
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: rs11145793; hg19: chr9-139274523; COSMIC: COSV53731358; COSMIC: COSV53731358;