6-30016475-G-A

Variant names:

• chr6-30016475-G-A
• rs9357092
• ENST00000444051.1:n.5395C>T

Variant summary

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

The ENST00000444051.1(POLR1HASP):​n.5395C>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 0.238 in 152,048 control chromosomes in the GnomAD database, including 4,709 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 0.24 (4709 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: POLR1HASP ENST00000444051.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 36 publications found

Genes affected

POLR1HASP (HGNC:):

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444051.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	NR_026751.2		n.714-13743C>T		intron	N/A
	POLR1HASP	NR_145416.1		n.809-2918C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000444051.1	TSL:1	n.5395C>T		non_coding_transcript_exon	Exon 2 of 2
	POLR1HASP	ENST00000420251.5	TSL:1	n.709-13743C>T		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.625+5192C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36138 AN: 151930 Hom.: 4709 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.211

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.238 AC: 36134 AN: 152048 Hom.: 4709 Cov.: 32 AF XY: 0.238 AC XY: 17695 AN XY: 74328

African (AFR) AF: 0.142 AC: 5891 AN: 41452

American (AMR) AF: 0.241 AC: 3684 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1525 AN: 5168

South Asian (SAS) AF: 0.162 AC: 782 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3725 AN: 10564

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19157 AN: 67970

Other (OTH) AF: 0.209 AC: 441 AN: 2114

Alfa AF: 0.260 Hom.: 15179

Bravo AF: 0.227

Asia WGS AF: 0.189 AC: 656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9357092; hg19: chr6-29984252;