chr6-149888640-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394057.1(RAET1E):ā€‹c.650A>Cā€‹(p.His217Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.0 ( 0 hom., cov: 26)
Failed GnomAD Quality Control

Consequence

RAET1E
NM_001394057.1 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.74
Variant links:
Genes affected
RAET1E (HGNC:16793): (retinoic acid early transcript 1E) This gene belong to the RAET1 family, which consists of major histocompatibility complex (MHC) class I-related genes located in a cluster on chromosome 6q24.2-q25.3. This and RAET1G protein differ from other RAET1 proteins in that they have type I membrane-spanning sequences at their C termini rather than glycosylphosphatidylinositol anchor sequences. This protein functions as a ligand for NKG2D receptor, which is expressed on the surface of several types of immune cells, and is involved in innate and adaptive immune responses. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Aug 2011]
RAET1E-AS1 (HGNC:48994): (RAET1E antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.052439272).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
RAET1ENM_001394057.1 linkuse as main transcriptc.650A>C p.His217Pro missense_variant 6/6 ENST00000357183.9
RAET1E-LRP11NR_182438.1 linkuse as main transcriptn.1068A>C non_coding_transcript_exon_variant 5/15
RAET1E-AS1NR_045126.1 linkuse as main transcriptn.885+24258T>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
RAET1EENST00000357183.9 linkuse as main transcriptc.650A>C p.His217Pro missense_variant 6/61 NM_001394057.1 P2Q8TD07-1
RAET1E-AS1ENST00000605899.1 linkuse as main transcriptn.114+2967T>G intron_variant, non_coding_transcript_variant 5
RAET1E-AS1ENST00000606915.1 linkuse as main transcriptn.889+24258T>G intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
130578
Hom.:
0
Cov.:
26
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
130578
Hom.:
0
Cov.:
26
AF XY:
0.00
AC XY:
0
AN XY:
61618
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 15, 2023The c.650A>C (p.H217P) alteration is located in exon 1 (coding exon 1) of the RAET1E gene. This alteration results from a A to C substitution at nucleotide position 650, causing the histidine (H) at amino acid position 217 to be replaced by a proline (P). 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
Benign
0.064
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.0090
DANN
Benign
0.50
DEOGEN2
Benign
0.0071
T;.
Eigen
Benign
-1.5
Eigen_PC
Benign
-1.6
FATHMM_MKL
Benign
0.011
N
LIST_S2
Benign
0.27
T;T
M_CAP
Benign
0.0019
T
MetaRNN
Benign
0.052
T;T
MetaSVM
Benign
-0.90
T
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.28
T
PROVEAN
Benign
0.91
N;N
REVEL
Benign
0.0080
Sift
Benign
0.31
T;T
Sift4G
Benign
0.39
T;T
Polyphen
0.0
B;B
Vest4
0.13
MutPred
0.46
Loss of sheet (P = 0.0104);.;
MVP
0.081
MPC
0.11
ClinPred
0.48
T
GERP RS
-1.5
Varity_R
0.079
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
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: chr6-150209776; API