6-29958195-A-T

Position:

• chr6-29958195-A-T

Variant summary

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

The ENST00000439514.1(HLA-W):​n.689-144A>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 0.319 in 152,422 control chromosomes in the GnomAD database, including 8,077 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 0.32 (8047 hom., cov: 32)
  • Exomes 𝑓: 0.32 (30 hom.)
• Consequence: HLA-W ENST00000439514.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HLA-W	ENST00000439514.1	n.689-144A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48445 AN: 151802 Hom.: 8045 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.323 AC: 163 AN: 504 Hom.: 30 AF XY: 0.322 AC XY: 101 AN XY: 314

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.333

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.250

Gnomad4 SAS exome AF: 0.321

Gnomad4 FIN exome AF: 0.395

Gnomad4 NFE exome AF: 0.281

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.319 AC: 48459 AN: 151918 Hom.: 8047 Cov.: 32 AF XY: 0.318 AC XY: 23620 AN XY: 74242

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.295

Alfa AF: 0.322 Hom.: 4452

Bravo AF: 0.316

Asia WGS AF: 0.236 AC: 817 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517701; hg19: chr6-29925972;