chr9-136390000-A-G

Position:

• chr9-136390000-A-G

Variant summary

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

The NM_003086.4(SNAPC4):​c.976-1409T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,290 control chromosomes in the GnomAD database, including 998 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 0.10 (998 hom., cov: 32)
• Consequence: SNAPC4 NM_003086.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SNAPC4	NM_003086.4	c.976-1409T>C		intron_variant		ENST00000684778.1	NP_003077.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SNAPC4	ENST00000684778.1	c.976-1409T>C		intron_variant			NM_003086.4	ENSP00000510559	P1

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15933 AN: 152172 Hom.: 987 Cov.: 32

Gnomad AFR AF: 0.0395

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0876

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.105 AC: 15965 AN: 152290 Hom.: 998 Cov.: 32 AF XY: 0.104 AC XY: 7738 AN XY: 74476

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.177

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.0876

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.0942

Alfa AF: 0.126 Hom.: 612

Bravo AF: 0.110

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.3
DANN	Benign	0.66

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: rs11145835; hg19: chr9-139284452;