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GeneBe

rs2395185

Variant summary

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

The ENST00000449413.1(HLA-DRB9):n.77-5303C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,038 control chromosomes in the GnomAD database, including 6,787 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 0.29 ( 6787 hom., cov: 32)

Consequence

HLA-DRB9
ENST00000449413.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.119
Variant links:
Genes affected
HLA-DRB9 (HGNC:4957): (major histocompatibility complex, class II, DR beta 9 (pseudogene))

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=-0.97).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DRB9ENST00000449413.1 linkuse as main transcriptn.77-5303C>A intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.291
AC:
44174
AN:
151918
Hom.:
6786
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.227
Gnomad AMI
AF:
0.417
Gnomad AMR
AF:
0.358
Gnomad ASJ
AF:
0.439
Gnomad EAS
AF:
0.342
Gnomad SAS
AF:
0.259
Gnomad FIN
AF:
0.235
Gnomad MID
AF:
0.275
Gnomad NFE
AF:
0.312
Gnomad OTH
AF:
0.308
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.291
AC:
44201
AN:
152038
Hom.:
6787
Cov.:
32
AF XY:
0.287
AC XY:
21331
AN XY:
74334
show subpopulations
Gnomad4 AFR
AF:
0.227
Gnomad4 AMR
AF:
0.358
Gnomad4 ASJ
AF:
0.439
Gnomad4 EAS
AF:
0.344
Gnomad4 SAS
AF:
0.258
Gnomad4 FIN
AF:
0.235
Gnomad4 NFE
AF:
0.312
Gnomad4 OTH
AF:
0.305
Alfa
AF:
0.314
Hom.:
13933
Bravo
AF:
0.307
Asia WGS
AF:
0.251
AC:
875
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
4.1
Dann
Benign
0.58

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: rs2395185; hg19: chr6-32433167; API