20-16731635-C-T

Variant names:

• chr20-16731635-C-T
• rs6111262
• NM_003092.5:c.-35-33C>T

Variant summary

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

The NM_003092.5(SNRPB2):​c.-35-33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,580,726 control chromosomes in the GnomAD database, including 47,077 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 (3305 hom., cov: 33)
  • Exomes 𝑓: 0.24 (43772 hom.)
• Consequence: SNRPB2 NM_003092.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 publications found

Genes affected

SNRPB2 (HGNC:11155): (small nuclear ribonucleoprotein polypeptide B2) The protein encoded by this gene associates with stem loop IV of U2 small nuclear ribonucleoprotein (U2 snRNP) in the presence of snRNP-A'. The encoded protein may play a role in pre-mRNA splicing. Autoantibodies from patients with systemic lupus erythematosus frequently recognize epitopes on the encoded protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003092.5. 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
	SNRPB2	NM_003092.5	MANE Select	c.-35-33C>T		intron	N/A	NP_003083.1
	SNRPB2	NM_198220.3		c.-35-33C>T		intron	N/A	NP_937863.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNRPB2	ENST00000246071.8	TSL:1 MANE Select	c.-35-33C>T		intron	N/A	ENSP00000246071.6
	SNRPB2	ENST00000377943.9	TSL:1	c.-35-33C>T		intron	N/A	ENSP00000367178.5
	SNRPB2	ENST00000478522.1	TSL:2	n.137-33C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28966 AN: 152004 Hom.: 3304 Cov.: 33

Gnomad AFR AF: 0.0646

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.204

GnomAD4 exome AF: 0.244 AC: 347991 AN: 1428604 Hom.: 43772 Cov.: 27 AF XY: 0.244 AC XY: 173734 AN XY: 711966

African (AFR) AF: 0.0550 AC: 1786 AN: 32500

American (AMR) AF: 0.203 AC: 8584 AN: 42308

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 7012 AN: 25606

East Asian (EAS) AF: 0.198 AC: 7764 AN: 39266

South Asian (SAS) AF: 0.213 AC: 17983 AN: 84500

European-Finnish (FIN) AF: 0.206 AC: 10946 AN: 53056

Middle Eastern (MID) AF: 0.226 AC: 1017 AN: 4494

European-Non Finnish (NFE) AF: 0.256 AC: 278863 AN: 1087998

Other (OTH) AF: 0.238 AC: 14036 AN: 58876

GnomAD4 genome AF: 0.191 AC: 28982 AN: 152122 Hom.: 3305 Cov.: 33 AF XY: 0.190 AC XY: 14118 AN XY: 74352

African (AFR) AF: 0.0646 AC: 2683 AN: 41518

American (AMR) AF: 0.202 AC: 3086 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3468

East Asian (EAS) AF: 0.223 AC: 1152 AN: 5166

South Asian (SAS) AF: 0.211 AC: 1016 AN: 4812

European-Finnish (FIN) AF: 0.204 AC: 2157 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17188 AN: 67970

Other (OTH) AF: 0.203 AC: 428 AN: 2108

Alfa AF: 0.236 Hom.: 6484

Bravo AF: 0.187

Asia WGS AF: 0.226 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.10
DANN	Benign	0.26
PhyloP100		-1.4
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: rs6111262; hg19: chr20-16712280;