Variant 9-99227771-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006808.3(SEC61B):c.102-128A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0665 in 654,270 control chromosomes in the GnomAD database, including 1,671 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.062 ( 336 hom., cov: 32)

Exomes 𝑓: 0.068 ( 1335 hom. )

Consequence

SEC61B
NM_006808.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.827

Variant links:

Genes affected

SEC61B (HGNC:16993): (SEC61 translocon subunit beta) The Sec61 complex is the central component of the protein translocation apparatus of the endoplasmic reticulum (ER) membrane. Oligomers of the Sec61 complex form a transmembrane channel where proteins are translocated across and integrated into the ER membrane. This complex consists of three membrane proteins- alpha, beta, and gamma. This gene encodes the beta-subunit protein. The Sec61 subunits are also observed in the post-ER compartment, suggesting that these proteins can escape the ER and recycle back. There is evidence for multiple polyadenylated sites for this transcript. [provided by RefSeq, Jul 2008]

SEC61B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BP6

Variant 9-99227771-A-G is Benign according to our data. Variant chr9-99227771-A-G is described in ClinVar as [Benign]. Clinvar id is 1183783.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SEC61B	NM_006808.3 linkuse as main transcript	c.102-128A>G		intron_variant		ENST00000223641.5	NP_006799.1	P60468
SEC61B	XM_047422662.1 linkuse as main transcript	c.55-128A>G		intron_variant			XP_047278618.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SEC61B	ENST00000223641.5 linkuse as main transcript	c.102-128A>G		intron_variant		1	NM_006808.3	ENSP00000223641.4		P60468
SEC61B	ENST00000498603.5 linkuse as main transcript	c.-61-128A>G		intron_variant		3		ENSP00000474122.1		S4R3B5

Frequencies

GnomAD3 genomes

AF:

0.0615

AC:

9357

AN:

152150

Hom.:

335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0390

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.0635

Gnomad ASJ

AF:

0.0542

Gnomad EAS

AF:

0.0100

Gnomad SAS

AF:

0.0598

Gnomad FIN

AF:

0.0547

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.0784

Gnomad OTH

AF:

0.0645

GnomAD4 exome

AF:

0.0680

AC:

34124

AN:

502002

Hom.:

1335

AF XY:

0.0676

AC XY:

17785

AN XY:

263128

show subpopulations

Gnomad4 AFR exome

AF:

0.0388

Gnomad4 AMR exome

AF:

0.0648

Gnomad4 ASJ exome

AF:

0.0493

Gnomad4 EAS exome

AF:

0.00981

Gnomad4 SAS exome

AF:

0.0635

Gnomad4 FIN exome

AF:

0.0560

Gnomad4 NFE exome

AF:

0.0780

Gnomad4 OTH exome

AF:

0.0678

GnomAD4 genome

AF:

0.0616

AC:

9375

AN:

152268

Hom.:

336

Cov.:

AF XY:

0.0603

AC XY:

4491

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.0395

Gnomad4 AMR

AF:

0.0633

Gnomad4 ASJ

AF:

0.0542

Gnomad4 EAS

AF:

0.0100

Gnomad4 SAS

AF:

0.0596

Gnomad4 FIN

AF:

0.0547

Gnomad4 NFE

AF:

0.0784

Gnomad4 OTH

AF:

0.0638

Alfa

AF:

0.0618

Hom.:

Bravo

AF:

0.0616

Asia WGS

AF:

0.0440

AC:

154

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 17, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

3.3

DANN

Benign

0.78

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over