rs1534166

Variant names:

• chr3-133818223-A-G
• rs1534166
• NM_001379313.1:c.602+1291A>G

Variant summary

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

The NM_001379313.1(SRPRB):​c.602+1291A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,164 control chromosomes in the GnomAD database, including 6,038 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 0.28 (6038 hom., cov: 32)
• Consequence: SRPRB NM_001379313.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 22 publications found

Genes affected

SRPRB (HGNC:24085): (SRP receptor subunit beta) The protein encoded by this gene has similarity to mouse protein which is a subunit of the signal recognition particle receptor (SR). This subunit is a transmembrane GTPase belonging to the GTPase superfamily. It anchors alpha subunit, a peripheral membrane GTPase, to the ER membrane. SR is required for the cotranslational targeting of both secretory and membrane proteins to the ER membrane. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001379313.1. 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
	SRPRB	NM_001379313.1	MANE Select	c.602+1291A>G		intron	N/A	NP_001366242.1	Q9Y5M8
	SRPRB	NM_021203.4		c.602+1291A>G		intron	N/A	NP_067026.3
	SRPRB	NR_163491.1		n.636+1291A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRPRB	ENST00000678299.1	MANE Select	c.602+1291A>G		intron	N/A	ENSP00000503923.1	Q9Y5M8
	SRPRB	ENST00000466490.7	TSL:5	c.602+1291A>G		intron	N/A	ENSP00000418401.1	Q9Y5M8
	SRPRB	ENST00000961954.1		c.524+1291A>G		intron	N/A	ENSP00000632013.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42438 AN: 152046 Hom.: 6030 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.279 AC: 42469 AN: 152164 Hom.: 6038 Cov.: 32 AF XY: 0.276 AC XY: 20538 AN XY: 74388

African (AFR) AF: 0.301 AC: 12483 AN: 41474

American (AMR) AF: 0.238 AC: 3634 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1210 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1076 AN: 5186

South Asian (SAS) AF: 0.225 AC: 1085 AN: 4820

European-Finnish (FIN) AF: 0.277 AC: 2939 AN: 10596

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19113 AN: 68008

Other (OTH) AF: 0.293 AC: 620 AN: 2116

Alfa AF: 0.283 Hom.: 28611

Bravo AF: 0.278

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.76
PhyloP100		0.090
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: rs1534166; hg19: chr3-133537067;