ENST00000420251.5:n.709-7843C>T

Variant names:

• chr6-30010575-G-A
• rs4713281
• ENST00000420251.5:n.709-7843C>T

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.709-7843C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 150,188 control chromosomes in the GnomAD database, including 4,591 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 (4591 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870
• Publications: 20 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.714-7843C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.709-7843C>T		intron_variant	Intron 5 of 5	1
POLR1HASP	ENST00000376797.7	n.626-744C>T		intron_variant	Intron 5 of 11	2
POLR1HASP	ENST00000422224.6	n.822+11092C>T		intron_variant	Intron 5 of 5	3

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35303 AN: 150078 Hom.: 4591 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.210

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.235 AC: 35299 AN: 150188 Hom.: 4591 Cov.: 32 AF XY: 0.236 AC XY: 17306 AN XY: 73412

African (AFR) AF: 0.131 AC: 5286 AN: 40352

American (AMR) AF: 0.234 AC: 3527 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 576 AN: 3444

East Asian (EAS) AF: 0.300 AC: 1524 AN: 5082

South Asian (SAS) AF: 0.165 AC: 776 AN: 4692

European-Finnish (FIN) AF: 0.359 AC: 3771 AN: 10516

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.282 AC: 19086 AN: 67748

Other (OTH) AF: 0.208 AC: 432 AN: 2080

Alfa AF: 0.252 Hom.: 4071

Bravo AF: 0.220

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.44
PhyloP100		0.087

Splicing

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

Other links and lift over

dbSNP: rs4713281; hg19: chr6-29978352;