6-30261680-C-T

Position:

• chr6-30261680-C-T

Variant summary

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

The NR_027822.1(HLA-L):​n.875C>T 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 0.269 in 1,363,488 control chromosomes in the GnomAD database, including 55,962 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 (6651 hom., cov: 31)
  • Exomes 𝑓: 0.27 (49311 hom.)
• Consequence: HLA-L NR_027822.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

HLA-L (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HLA-L	NR_027822.1	n.875C>T		non_coding_transcript_exon_variant	5/7
HCG17	NR_052012.1	n.127-7216G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-L	ENST00000420110.1	n.988C>T		non_coding_transcript_exon_variant	5/5	6
HLA-L	ENST00000463348.6	n.884C>T		non_coding_transcript_exon_variant	5/7	6
HLA-L	ENST00000482052.6	n.1102C>T		non_coding_transcript_exon_variant	4/6	6

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43273 AN: 151520 Hom.: 6643 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.309

GnomAD3 exomes AF: 0.322 AC: 80139 AN: 248710 Hom.: 14589 AF XY: 0.321 AC XY: 43340 AN XY: 134822

Gnomad AFR exome AF: 0.293

Gnomad AMR exome AF: 0.469

Gnomad ASJ exome AF: 0.395

Gnomad EAS exome AF: 0.455

Gnomad SAS exome AF: 0.454

Gnomad FIN exome AF: 0.268

Gnomad NFE exome AF: 0.227

Gnomad OTH exome AF: 0.318

GnomAD4 exome AF: 0.267 AC: 323531 AN: 1211850 Hom.: 49311 Cov.: 22 AF XY: 0.272 AC XY: 167325 AN XY: 614242

Gnomad4 AFR exome AF: 0.295

Gnomad4 AMR exome AF: 0.462

Gnomad4 ASJ exome AF: 0.391

Gnomad4 EAS exome AF: 0.525

Gnomad4 SAS exome AF: 0.455

Gnomad4 FIN exome AF: 0.265

Gnomad4 NFE exome AF: 0.223

Gnomad4 OTH exome AF: 0.293

GnomAD4 genome AF: 0.286 AC: 43315 AN: 151638 Hom.: 6651 Cov.: 31 AF XY: 0.292 AC XY: 21663 AN XY: 74082

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.489

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.311

Alfa AF: 0.256 Hom.: 2287

Bravo AF: 0.294

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.7
DANN	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2023478; hg19: chr6-30229457;