rs3094073

Positions:

• chr6-30263447-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

Genes affected

HLA-L (HGNC:):

ACMG classification

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	n.1118G>A		non_coding_transcript_exon_variant	7/7
HCG17	NR_052012.1	n.127-8983C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-L	ENST00000463348.6	n.1127G>A		non_coding_transcript_exon_variant	7/7	6
HLA-L	ENST00000701167.1	n.1845G>A		non_coding_transcript_exon_variant	7/7
HLA-L	ENST00000702262.1	n.1331G>A		non_coding_transcript_exon_variant	8/8

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18173 AN: 152072 Hom.: 1209 Cov.: 32

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

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.: 0 AF XY: 0.121 AC XY: 25891 AN XY: 213572

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.: 32 AF XY: 0.115 AC XY: 8556 AN XY: 74424

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

Other links and lift over

dbSNP: rs3094073; hg19: chr6-30231224; COSMIC: COSV69717041;