chr3-133820730-A-C

Variant names:

• chr3-133820730-A-C
• rs10512913
• NM_001379313.1:c.*964A>C

Variant summary

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

The NM_001379313.1(SRPRB):​c.*964A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,194 control chromosomes in the GnomAD database, including 3,506 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 (3506 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SRPRB NM_001379313.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRPRB	NM_001379313.1	c.*964A>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000678299.1	NP_001366242.1
SRPRB	NM_021203.4	c.*964A>C		3_prime_UTR_variant	Exon 8 of 8		NP_067026.3
SRPRB	NR_163491.1	n.904+910A>C		intron_variant	Intron 7 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRPRB	ENST00000678299.1	c.*964A>C		3_prime_UTR_variant	Exon 7 of 7		NM_001379313.1	ENSP00000503923.1
SRPRB	ENST00000466490.7	c.*964A>C		3_prime_UTR_variant	Exon 8 of 8	5		ENSP00000418401.1
SRPRB	ENST00000466636.1	n.*54+910A>C		intron_variant	Intron 4 of 4	3		ENSP00000417316.1

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28439 AN: 152078 Hom.: 3505 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0427

Gnomad SAS AF: 0.0904

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.203

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.187 AC: 28432 AN: 152194 Hom.: 3506 Cov.: 32 AF XY: 0.185 AC XY: 13740 AN XY: 74388

African (AFR) AF: 0.0448 AC: 1861 AN: 41546

American (AMR) AF: 0.162 AC: 2478 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 847 AN: 3470

East Asian (EAS) AF: 0.0428 AC: 222 AN: 5190

South Asian (SAS) AF: 0.0913 AC: 441 AN: 4828

European-Finnish (FIN) AF: 0.339 AC: 3579 AN: 10560

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18131 AN: 67994

Other (OTH) AF: 0.200 AC: 422 AN: 2110

Alfa AF: 0.232 Hom.: 13365

Bravo AF: 0.169

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		0.035
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: rs10512913; hg19: chr3-133539574;