6-30041219-C-T

Variant names:

• chr6-30041219-C-T
• rs9261212
• ENST00000420251.5:n.438-5236G>A

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.438-5236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.899 in 152,244 control chromosomes in the GnomAD database, including 61,590 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 0.90 (61590 hom., cov: 31)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-5236G>A		intron_variant	Intron 3 of 5
POLR1HASP	NR_145416.1	n.443-5236G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.438-5236G>A		intron_variant	Intron 3 of 5	1
POLR1HASP	ENST00000437417.5	n.977-5236G>A		intron_variant	Intron 2 of 5	1
POLR1HASP	ENST00000376797.7	n.260-5236G>A		intron_variant	Intron 2 of 11	2

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136687 AN: 152126 Hom.: 61527 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.899 AC: 136809 AN: 152244 Hom.: 61590 Cov.: 31 AF XY: 0.900 AC XY: 66967 AN XY: 74440

African (AFR) AF: 0.919 AC: 38194 AN: 41544

American (AMR) AF: 0.917 AC: 14009 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3148 AN: 3470

East Asian (EAS) AF: 0.987 AC: 5116 AN: 5184

South Asian (SAS) AF: 0.945 AC: 4564 AN: 4830

European-Finnish (FIN) AF: 0.890 AC: 9436 AN: 10600

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59321 AN: 68012

Other (OTH) AF: 0.895 AC: 1893 AN: 2116

Alfa AF: 0.885 Hom.: 37114

Bravo AF: 0.903

Asia WGS AF: 0.961 AC: 3341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.51
DANN	Benign	0.28
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs9261212; hg19: chr6-30008996;