rs1534166

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRPRB	NM_001379313.1	c.602+1291A>G		intron_variant	Intron 6 of 6	ENST00000678299.1	NP_001366242.1
SRPRB	NM_021203.4	c.602+1291A>G		intron_variant	Intron 7 of 7		NP_067026.3
SRPRB	NR_163491.1	n.636+1291A>G		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRPRB	ENST00000678299.1	c.602+1291A>G		intron_variant	Intron 6 of 6		NM_001379313.1	ENSP00000503923.1

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

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.293

Alfa AF: 0.286 Hom.: 14310

Bravo AF: 0.278

Asia WGS AF: 0.189 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.76

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: rs1534166; hg19: chr3-133537067;