chr6-34771949-T-G

Variant names:

• chr6-34771949-T-G
• rs9462015
• NM_003093.3:c.356-1497T>G

Variant summary

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

The NM_003093.3(SNRPC):​c.356-1497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,996 control chromosomes in the GnomAD database, including 16,398 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 0.44 (16398 hom., cov: 32)
• Consequence: SNRPC NM_003093.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 16 publications found

Genes affected

SNRPC (HGNC:11157): (small nuclear ribonucleoprotein polypeptide C) This gene encodes one of the specific protein components of the U1 small nuclear ribonucleoprotein (snRNP) particle required for the formation of the spliceosome. The encoded protein participates in the processing of nuclear precursor messenger RNA splicing. snRNP particles are attacked by autoantibodies frequently produced by patients with connective tissue diseases. The genome contains several pseudogenes of this functional gene. Alternative splicing results in a non-coding transcript variant.[provided by RefSeq, Oct 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003093.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPC	NM_003093.3	MANE Select	c.356-1497T>G		intron	N/A	NP_003084.1	P09234
	SNRPC	NR_029472.2		n.352-1497T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPC	ENST00000244520.10	TSL:1 MANE Select	c.356-1497T>G		intron	N/A	ENSP00000244520.5	P09234
	SNRPC	ENST00000374017.3	TSL:2	c.419-1497T>G		intron	N/A	ENSP00000363129.3	A0A0A0MRR7
	SNRPC	ENST00000909265.1		c.356-1002T>G		intron	N/A	ENSP00000579324.1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66512 AN: 151878 Hom.: 16348 Cov.: 32

Gnomad AFR AF: 0.674

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.448

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

GnomAD4 genome AF: 0.438 AC: 66610 AN: 151996 Hom.: 16398 Cov.: 32 AF XY: 0.437 AC XY: 32484 AN XY: 74284

African (AFR) AF: 0.675 AC: 27974 AN: 41454

American (AMR) AF: 0.357 AC: 5451 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1460 AN: 3466

East Asian (EAS) AF: 0.456 AC: 2357 AN: 5168

South Asian (SAS) AF: 0.317 AC: 1531 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3558 AN: 10534

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 23007 AN: 67968

Other (OTH) AF: 0.449 AC: 949 AN: 2112

Alfa AF: 0.341 Hom.: 5274

Bravo AF: 0.452

Asia WGS AF: 0.364 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.60
PhyloP100		-0.16
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: rs9462015; hg19: chr6-34739726;