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GeneBe

rs2187668

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_002122.5(HLA-DQA1):c.82+567C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00335 in 127434 control chromosomes in the gnomAD Genomes database, including 9 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 0.0034 ( 9 hom., cov: 20)

Consequence

HLA-DQA1
NM_002122.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0980

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BS2
?
High Homozygotes in GnomAd at 9 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
HLA-DQA1NM_002122.5 linkuse as main transcriptc.82+567C>T intron_variant ENST00000343139.11
LOC124901301XR_007059544.1 linkuse as main transcriptn.2056G>A non_coding_transcript_exon_variant 2/2
HLA-DQA1XM_006715079.5 linkuse as main transcriptc.82+567C>T intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
HLA-DQA1ENST00000343139.11 linkuse as main transcriptc.82+567C>T intron_variant NM_002122.5 P1

Frequencies

GnomAD3 genomes
AF:
0.00335
AC:
427
AN:
127434
Hom.:
9
Cov.:
20
show subpopulations
Gnomad AFR
AF:
0.00113
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00247
Gnomad ASJ
AF:
0.00256
Gnomad EAS
AF:
0.00459
Gnomad SAS
AF:
0.00474
Gnomad FIN
AF:
0.00135
Gnomad MID
AF:
0.0165
Gnomad NFE
AF:
0.00492
Gnomad OTH
AF:
0.00646
Alfa
AF:
0.116
Hom.:
1884
Asia WGS
AF:
0.0670
AC:
233
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
7.6
Dann
Benign
0.33

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.

Other links and lift over

dbSNP: rs2187668; hg19: chr6-32605884;