rs62391965

Variant summary

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

The NM_001384290.1(HLA-G):​c.619+154C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0518 in 152,086 control chromosomes in the GnomAD database, including 370 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 0.052 ( 370 hom., cov: 31)

Consequence

HLA-G
NM_001384290.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82
Variant links:
Genes affected
HLA-G (HGNC:4964): (major histocompatibility complex, class I, G) HLA-G belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. HLA-G is expressed on fetal derived placental cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon one encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domain, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exon 6 encodes the cytoplasmic tail. [provided by RefSeq, Jul 2008]

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 (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HLA-GNM_001384290.1 linkuse as main transcriptc.619+154C>A intron_variant ENST00000360323.11 NP_001371219.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HLA-GENST00000360323.11 linkuse as main transcriptc.619+154C>A intron_variant NM_001384290.1 ENSP00000353472 P2P17693-1

Frequencies

GnomAD3 genomes
AF:
0.0519
AC:
7883
AN:
151968
Hom.:
368
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0123
Gnomad AMI
AF:
0.0976
Gnomad AMR
AF:
0.0440
Gnomad ASJ
AF:
0.0568
Gnomad EAS
AF:
0.188
Gnomad SAS
AF:
0.164
Gnomad FIN
AF:
0.0389
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0607
Gnomad OTH
AF:
0.0522
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0518
AC:
7884
AN:
152086
Hom.:
370
Cov.:
31
AF XY:
0.0542
AC XY:
4033
AN XY:
74342
show subpopulations
Gnomad4 AFR
AF:
0.0122
Gnomad4 AMR
AF:
0.0440
Gnomad4 ASJ
AF:
0.0568
Gnomad4 EAS
AF:
0.187
Gnomad4 SAS
AF:
0.165
Gnomad4 FIN
AF:
0.0389
Gnomad4 NFE
AF:
0.0607
Gnomad4 OTH
AF:
0.0526
Alfa
AF:
0.0431
Hom.:
25
Bravo
AF:
0.0482
Asia WGS
AF:
0.137
AC:
476
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
6.9
DANN
Benign
0.72

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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.

Other links and lift over

dbSNP: rs62391965; hg19: chr6-29796749; API