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GeneBe

rs3823321

chr6-29826690-G-Achr6-29826690-G-T

Variant summary

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

The NM_001384280.1(HLA-G):c.-37+143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,168 control chromosomes in the GnomAD database, including 1,959 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 0.15 ( 1959 hom., cov: 33)

Consequence

HLA-G
NM_001384280.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.235
Variant links:
Genes affected

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-GNM_001384280.1 linkuse as main transcriptc.-37+143G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.145
AC:
22099
AN:
152050
Hom.:
1953
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.224
Gnomad AMI
AF:
0.105
Gnomad AMR
AF:
0.174
Gnomad ASJ
AF:
0.110
Gnomad EAS
AF:
0.304
Gnomad SAS
AF:
0.204
Gnomad FIN
AF:
0.0875
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.0861
Gnomad OTH
AF:
0.153
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.145
AC:
22120
AN:
152168
Hom.:
1959
Cov.:
33
AF XY:
0.148
AC XY:
10976
AN XY:
74394
show subpopulations
Gnomad4 AFR
AF:
0.224
Gnomad4 AMR
AF:
0.174
Gnomad4 ASJ
AF:
0.110
Gnomad4 EAS
AF:
0.303
Gnomad4 SAS
AF:
0.203
Gnomad4 FIN
AF:
0.0875
Gnomad4 NFE
AF:
0.0861
Gnomad4 OTH
AF:
0.159
Alfa
AF:
0.0434
Hom.:
46
Bravo
AF:
0.154
Asia WGS
AF:
0.327
AC:
1136
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
Cadd
Benign
6.3
Dann
Benign
0.52

Splicing

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: rs3823321; hg19: chr6-29794467; API