Variant chr6-30263447-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_027822.1(HLA-L):n.1118G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 526,342 control chromosomes in the GnomAD database, including 4,445 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 0.12 ( 1215 hom., cov: 32)

Exomes 𝑓: 0.12 ( 3230 hom. )

Consequence

HLA-L
NR_027822.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0650

Variant links:

Genes affected

HLA-L (HGNC:):

HLA-L links:

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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-L	NR_027822.1 linkuse as main transcript	n.1118G>A		non_coding_transcript_exon_variant	7/7
HCG17	NR_052012.1 linkuse as main transcript	n.127-8983C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
HLA-L	ENST00000463348.6 linkuse as main transcript	n.1127G>A	non_coding_transcript_exon_variant	7/7	6
HLA-L	ENST00000701167.1 linkuse as main transcript	n.1845G>A	non_coding_transcript_exon_variant	7/7
HLA-L	ENST00000702262.1 linkuse as main transcript	n.1331G>A	non_coding_transcript_exon_variant	8/8

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18173

AN:

152072

Hom.:

1209

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.170

Gnomad AMR

AF:

0.0910

Gnomad ASJ

AF:

0.0638

Gnomad EAS

AF:

0.0493

Gnomad SAS

AF:

0.0818

Gnomad FIN

AF:

0.0944

Gnomad MID

AF:

0.0828

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.100

GnomAD3 exomes

AF:

0.116

AC:

28086

AN:

242154

Hom.:

1936

AF XY:

0.118

AC XY:

15424

AN XY:

131098

show subpopulations

Gnomad AFR exome

AF:

0.103

Gnomad AMR exome

AF:

0.104

Gnomad ASJ exome

AF:

0.0598

Gnomad EAS exome

AF:

0.0506

Gnomad SAS exome

AF:

0.0984

Gnomad FIN exome

AF:

0.0961

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.115

GnomAD4 exome

AF:

0.121

AC:

45404

AN:

374150

Hom.:

3230

Cov.:

AF XY:

0.121

AC XY:

25891

AN XY:

213572

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.102

Gnomad4 ASJ exome

AF:

0.0629

Gnomad4 EAS exome

AF:

0.0555

Gnomad4 SAS exome

AF:

0.103

Gnomad4 FIN exome

AF:

0.101

Gnomad4 NFE exome

AF:

0.145

Gnomad4 OTH exome

AF:

0.118

GnomAD4 genome

AF:

0.120

AC:

18203

AN:

152192

Hom.:

1215

Cov.:

AF XY:

0.115

AC XY:

8556

AN XY:

74424

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.0909

Gnomad4 ASJ

AF:

0.0638

Gnomad4 EAS

AF:

0.0496

Gnomad4 SAS

AF:

0.0831

Gnomad4 FIN

AF:

0.0944

Gnomad4 NFE

AF:

0.151

Gnomad4 OTH

AF:

0.104

Alfa

AF:

0.141

Hom.:

3052

Bravo

AF:

0.119

Asia WGS

AF:

0.0750

AC:

262

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.6

DANN

Benign

0.35

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over