rs4122189

Variant summary

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

The NR_026791.1(HCG27):​n.124-2222C>T 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 0.229 in 152,150 control chromosomes in the GnomAD database, including 4,188 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 0.23 ( 4187 hom., cov: 32)
Exomes 𝑓: 0.16 ( 1 hom. )

Consequence

HCG27
NR_026791.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.878
Variant links:
Genes affected
HCG27 (HGNC:27366): (HLA complex group 27)

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=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
HCG27NR_026791.1 linkuse as main transcriptn.124-2222C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
HCG27ENST00000383331.4 linkuse as main transcriptn.124-2222C>T intron_variant, non_coding_transcript_variant 1
ENST00000606909.1 linkuse as main transcript downstream_gene_variant 5

Frequencies

GnomAD3 genomes
AF:
0.229
AC:
34848
AN:
151968
Hom.:
4182
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.182
Gnomad AMI
AF:
0.112
Gnomad AMR
AF:
0.298
Gnomad ASJ
AF:
0.274
Gnomad EAS
AF:
0.394
Gnomad SAS
AF:
0.154
Gnomad FIN
AF:
0.272
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.229
Gnomad OTH
AF:
0.212
GnomAD4 exome
AF:
0.156
AC:
10
AN:
64
Hom.:
1
Cov.:
0
AF XY:
0.125
AC XY:
6
AN XY:
48
show subpopulations
Gnomad4 AMR exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.250
Gnomad4 NFE exome
AF:
0.180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.229
AC:
34863
AN:
152086
Hom.:
4187
Cov.:
32
AF XY:
0.233
AC XY:
17327
AN XY:
74336
show subpopulations
Gnomad4 AFR
AF:
0.181
Gnomad4 AMR
AF:
0.299
Gnomad4 ASJ
AF:
0.274
Gnomad4 EAS
AF:
0.394
Gnomad4 SAS
AF:
0.153
Gnomad4 FIN
AF:
0.272
Gnomad4 NFE
AF:
0.229
Gnomad4 OTH
AF:
0.216
Alfa
AF:
0.232
Hom.:
7854
Bravo
AF:
0.231
Asia WGS
AF:
0.251
AC:
874
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
5.0
DANN
Benign
0.72

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: rs4122189; hg19: chr6-31167927; API