Variant 6-150025396-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_130900.3(RAET1L):c.76A>G(p.Arg26Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,612,468 control chromosomes in the GnomAD database, including 161,832 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.45 ( 15375 hom., cov: 33)

Exomes 𝑓: 0.45 ( 146457 hom. )

Consequence

RAET1L
NM_130900.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Variant links:

Genes affected

RAET1L (HGNC:16798): (retinoic acid early transcript 1L) RAET1L belongs to the RAET1 family of major histocompatibility complex (MHC) class I-related genes, which are located within a 180-kb cluster on chromosome 6q24.2-q25.3. The REAT1 genes encode glycoproteins that contain extracellular alpha-1 and alpha-2 domains, but they lack the membrane proximal Ig-like alpha-3 domain. Most RAET1 glycoproteins are anchored to the membrane via glycosylphosphatidylinositol (GPI) linkage (Radosavljevic et al., 2002 [PubMed 11827464]).[supplied by OMIM, Mar 2008]

RAET1L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=2.1800399E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAET1L	NM_130900.3 linkuse as main transcript	c.76A>G	p.Arg26Gly	missense_variant	1/5	ENST00000367341.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAET1L	ENST00000367341.6 linkuse as main transcript	c.76A>G	p.Arg26Gly	missense_variant	1/5	1	NM_130900.3	P1
RAET1L	ENST00000286380.2 linkuse as main transcript	c.76A>G	p.Arg26Gly	missense_variant	1/4	1		P1

Frequencies

GnomAD3 genomes

AF:

0.446

AC:

67728

AN:

151996

Hom.:

15360

Cov.:

show subpopulations

Gnomad AFR

AF:

0.475

Gnomad AMI

AF:

0.419

Gnomad AMR

AF:

0.408

Gnomad ASJ

AF:

0.408

Gnomad EAS

AF:

0.231

Gnomad SAS

AF:

0.421

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.454

Gnomad OTH

AF:

0.444

GnomAD3 exomes

AF:

0.421

AC:

105457

AN:

250320

Hom.:

22843

AF XY:

0.422

AC XY:

57160

AN XY:

135362

show subpopulations

Gnomad AFR exome

AF:

0.478

Gnomad AMR exome

AF:

0.388

Gnomad ASJ exome

AF:

0.421

Gnomad EAS exome

AF:

0.221

Gnomad SAS exome

AF:

0.414

Gnomad FIN exome

AF:

0.466

Gnomad NFE exome

AF:

0.449

Gnomad OTH exome

AF:

0.426

GnomAD4 exome

AF:

0.446

AC:

650677

AN:

1460354

Hom.:

146457

Cov.:

AF XY:

0.445

AC XY:

323021

AN XY:

726460

show subpopulations

Gnomad4 AFR exome

AF:

0.477

Gnomad4 AMR exome

AF:

0.388

Gnomad4 ASJ exome

AF:

0.418

Gnomad4 EAS exome

AF:

0.262

Gnomad4 SAS exome

AF:

0.414

Gnomad4 FIN exome

AF:

0.459

Gnomad4 NFE exome

AF:

0.457

Gnomad4 OTH exome

AF:

0.434

GnomAD4 genome

AF:

0.446

AC:

67781

AN:

152114

Hom.:

15375

Cov.:

AF XY:

0.443

AC XY:

32925

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.475

Gnomad4 AMR

AF:

0.407

Gnomad4 ASJ

AF:

0.408

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.420

Gnomad4 FIN

AF:

0.465

Gnomad4 NFE

AF:

0.454

Gnomad4 OTH

AF:

0.445

Alfa

AF:

0.448

Hom.:

8025

Bravo

AF:

0.442

TwinsUK

AF:

0.457

AC:

1696

ALSPAC

AF:

0.445

AC:

1716

ESP6500AA

AF:

0.474

AC:

2088

ESP6500EA

AF:

0.450

AC:

3871

ExAC

AF:

0.422

AC:

51216

Asia WGS

AF:

0.366

AC:

1272

AN:

3478

EpiCase

AF:

0.445

EpiControl

AF:

0.450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.051

BayesDel_addAF

Benign

-0.85

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.40

DANN

Benign

0.18

DEOGEN2

Benign

0.00063

T;T

Eigen

Benign

-1.7

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.00038

LIST_S2

Benign

0.44

.;T

MetaRNN

Benign

0.00022

T;T

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.27

PROVEAN

Benign

0.64

N;N

REVEL

Benign

0.010

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;T

Polyphen

0.0

B;B

Vest4

0.016

MPC

0.023

ClinPred

0.0033

GERP RS

0.43

Varity_R

0.057

gMVP

0.12

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over