10-12133304-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018144.4(SEC61A2):​c.71G>A​(p.Arg24Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000145 in 1,379,524 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

SEC61A2
NM_018144.4 missense

Scores

2
7
10

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 9.53
Variant links:
Genes affected
SEC61A2 (HGNC:17702): (SEC61 translocon subunit alpha 2) The protein encoded by this gene has similarity to a mouse protein which suggests a role in the insertion of secretory and membrane polypeptides into the endoplasmic reticulum. It may also be required for the assembly of membrane and secretory proteins. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SEC61A2NM_018144.4 linkc.71G>A p.Arg24Lys missense_variant Exon 2 of 12 ENST00000298428.14 NP_060614.2 Q9H9S3-1Q8TC24

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SEC61A2ENST00000298428.14 linkc.71G>A p.Arg24Lys missense_variant Exon 2 of 12 1 NM_018144.4 ENSP00000298428.9 Q9H9S3-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000145
AC:
2
AN:
1379524
Hom.:
0
Cov.:
22
AF XY:
0.00000145
AC XY:
1
AN XY:
690714
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000192
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Mar 08, 2024
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.71G>A (p.R24K) alteration is located in exon 2 (coding exon 2) of the SEC61A2 gene. This alteration results from a G to A substitution at nucleotide position 71, causing the arginine (R) at amino acid position 24 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.34
BayesDel_addAF
Uncertain
0.059
T
BayesDel_noAF
Benign
-0.15
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.031
T;.;.;T;.;T;.
Eigen
Benign
0.15
Eigen_PC
Uncertain
0.35
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Uncertain
0.97
D;D;D;D;D;D;D
M_CAP
Benign
0.0026
T
MetaRNN
Uncertain
0.46
T;T;T;T;T;T;T
MetaSVM
Benign
-0.90
T
MutationAssessor
Uncertain
2.2
.;M;.;M;M;.;.
PrimateAI
Pathogenic
0.87
D
PROVEAN
Benign
-1.6
N;N;N;N;N;N;N
REVEL
Benign
0.21
Sift
Benign
0.20
T;T;T;T;T;T;T
Sift4G
Benign
0.23
T;T;T;T;T;T;T
Polyphen
0.0
.;.;.;B;B;.;.
Vest4
0.65
MutPred
0.39
Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);Gain of methylation at R24 (P = 0.004);
MVP
0.32
MPC
0.88
ClinPred
0.83
D
GERP RS
5.6
Varity_R
0.30
gMVP
0.89

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-12175303; API