rs11145793

chr9-136380071-G-Achr9-136380071-G-C

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNAPC4	NM_003086.4	c.2500-207C>T		intron_variant		ENST00000684778.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNAPC4	ENST00000684778.1	c.2500-207C>T		intron_variant			NM_003086.4	P1
SNAPC4	ENST00000298532.2	c.2500-207C>T		intron_variant		1		P1
SNAPC4	ENST00000637388.2	c.2500-207C>T		intron_variant		5		P1
SNAPC4	ENST00000689006.1	c.*1713-207C>T		intron_variant, NMD_transcript_variant

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.269

Gnomad4 ASJ AF: 0.208

Gnomad4 EAS AF: 0.0519

Gnomad4 SAS AF: 0.158

Gnomad4 FIN AF: 0.278

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.218

Alfa AF: 0.226 Hom.: 2501

Bravo AF: 0.203

Asia WGS AF: 0.126 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	14
Dann	Benign	0.67

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: rs11145793; hg19: chr9-139274523; COSMIC: COSV53731358; COSMIC: COSV53731358;