rs4313034

Variant names:

• chr6-30006148-C-T
• rs4313034
• ENST00000420251.5:n.709-3416G>A

Variant summary

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

The ENST00000458060.1(ENSG00000237669):​n.969G>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 0.787 in 188,392 control chromosomes in the GnomAD database, including 58,914 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 0.78 (46622 hom., cov: 32)
  • Exomes 𝑓: 0.82 (12292 hom.)
• Consequence: ENSG00000237669 ENST00000458060.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

Genes affected

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ENSG00000237669 (HGNC:):

HLA-J (HGNC:4967): (major histocompatibility complex, class I, J (pseudogene)) This major histocompatibility complex gene represents a transcribed pseudogene, possibly derived from HLA-A. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-J	NR_024240.1	n.169+9C>T		intron_variant	Intron 1 of 6
POLR1HASP	NR_026751.2	n.714-3416G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.709-3416G>A		intron_variant	Intron 5 of 5	1
ENSG00000237669	ENST00000458060.1	n.969G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
POLR1HASP	ENST00000376797.7	n.1346+1075G>A		intron_variant	Intron 10 of 11	2

Frequencies

GnomAD3 genomes AF: 0.780 AC: 118574 AN: 151942 Hom.: 46584 Cov.: 32

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.761

GnomAD4 exome AF: 0.816 AC: 29655 AN: 36332 Hom.: 12292 Cov.: 0 AF XY: 0.818 AC XY: 15161 AN XY: 18530

Gnomad4 AFR exome AF: 0.745

Gnomad4 AMR exome AF: 0.751

Gnomad4 ASJ exome AF: 0.776

Gnomad4 EAS exome AF: 0.841

Gnomad4 SAS exome AF: 0.814

Gnomad4 FIN exome AF: 0.840

Gnomad4 NFE exome AF: 0.821

Gnomad4 OTH exome AF: 0.790

GnomAD4 genome AF: 0.780 AC: 118664 AN: 152060 Hom.: 46622 Cov.: 32 AF XY: 0.783 AC XY: 58209 AN XY: 74334

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.866

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.764

Alfa AF: 0.807 Hom.: 34538

Bravo AF: 0.767

Asia WGS AF: 0.817 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4313034; hg19: chr6-29973925;