ENST00000849678.1:n.589-19470T>G

Variant names:

• chr6-29966386-A-C
• rs6935053
• ENST00000849678.1:n.589-19470T>G

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-19470T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,844 control chromosomes in the GnomAD database, including 5,653 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 0.26 (5653 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 20 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849678.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849678.1		n.589-19470T>G		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+10217T>G		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-9636T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40080 AN: 151728 Hom.: 5652 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.264 AC: 40079 AN: 151844 Hom.: 5653 Cov.: 32 AF XY: 0.264 AC XY: 19565 AN XY: 74188

African (AFR) AF: 0.202 AC: 8366 AN: 41328

American (AMR) AF: 0.254 AC: 3886 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 658 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1614 AN: 5166

South Asian (SAS) AF: 0.163 AC: 788 AN: 4826

European-Finnish (FIN) AF: 0.362 AC: 3806 AN: 10524

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.296 AC: 20132 AN: 67934

Other (OTH) AF: 0.239 AC: 503 AN: 2106

Alfa AF: 0.275 Hom.: 4448

Asia WGS AF: 0.202 AC: 697 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.0
DANN	Benign	0.23
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs6935053; hg19: chr6-29934163;