rs892666

Positions:

• chr6-29956951-T-C

Variant summary

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

The ENST00000439514.1(HLA-W):​n.261+95T>C 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 0.645 in 150,694 control chromosomes in the GnomAD database, including 31,457 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 0.65 (31446 hom., cov: 30)
  • Exomes 𝑓: 0.58 (11 hom.)
• Consequence: HLA-W ENST00000439514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22

Genes affected

HLA-W (HGNC:23425): (major histocompatibility complex, class I, W (pseudogene))

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HLA-W	ENST00000439514.1	n.261+95T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97118 AN: 150520 Hom.: 31430 Cov.: 30

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.633

GnomAD4 exome AF: 0.581 AC: 36 AN: 62 Hom.: 11 AF XY: 0.571 AC XY: 24 AN XY: 42

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.800

GnomAD4 genome AF: 0.645 AC: 97163 AN: 150632 Hom.: 31446 Cov.: 30 AF XY: 0.640 AC XY: 47079 AN XY: 73612

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.551

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.628

Alfa AF: 0.661 Hom.: 14264

Bravo AF: 0.652

Asia WGS AF: 0.507 AC: 1759 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892666; hg19: chr6-29924728;