rs4313034

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849694.1(POLR1HASP):​n.1816G>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: POLR1HASP ENST00000849694.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454
• Publications: 38 publications found

Genes affected

POLR1HASP (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]

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849694.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-J	NR_024240.1		n.169+9C>T		intron	N/A
	POLR1HASP	NR_026751.2		n.714-3416G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.709-3416G>A		intron	N/A
	ENSG00000237669	ENST00000458060.1	TSL:6	n.969G>A		non_coding_transcript_exon	Exon 1 of 1
	POLR1HASP	ENST00000849694.1		n.1816G>A		non_coding_transcript_exon	Exon 5 of 5

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

African (AFR) AF: 0.745 AC: 152 AN: 204

American (AMR) AF: 0.751 AC: 771 AN: 1026

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 559 AN: 720

East Asian (EAS) AF: 0.841 AC: 222 AN: 264

South Asian (SAS) AF: 0.814 AC: 3965 AN: 4870

European-Finnish (FIN) AF: 0.840 AC: 1473 AN: 1754

Middle Eastern (MID) AF: 0.832 AC: 213 AN: 256

European-Non Finnish (NFE) AF: 0.821 AC: 20480 AN: 24934

Other (OTH) AF: 0.790 AC: 1820 AN: 2304

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

African (AFR) AF: 0.695 AC: 28799 AN: 41456

American (AMR) AF: 0.775 AC: 11842 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2704 AN: 3468

East Asian (EAS) AF: 0.838 AC: 4327 AN: 5166

South Asian (SAS) AF: 0.787 AC: 3790 AN: 4814

European-Finnish (FIN) AF: 0.866 AC: 9177 AN: 10592

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55342 AN: 67970

Other (OTH) AF: 0.764 AC: 1613 AN: 2110

Alfa AF: 0.795 Hom.: 69673

Bravo AF: 0.767

Asia WGS AF: 0.817 AC: 2840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		-0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4313034;

hg19: chr6-29973925;