rs4713274

Variant names:

• chr6-29969716-G-C
• rs4713274
• ENST00000849678.1:n.589-22800C>G

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-22800C>G 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 151,924 control chromosomes in the GnomAD database, including 4,742 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 0.23 (4742 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.942
• Publications: 14 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.28 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849678.1		n.589-22800C>G		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+6887C>G		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-12966C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35674 AN: 151808 Hom.: 4742 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.235 AC: 35670 AN: 151924 Hom.: 4742 Cov.: 32 AF XY: 0.235 AC XY: 17461 AN XY: 74246

African (AFR) AF: 0.130 AC: 5374 AN: 41368

American (AMR) AF: 0.238 AC: 3632 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1510 AN: 5178

South Asian (SAS) AF: 0.152 AC: 730 AN: 4816

European-Finnish (FIN) AF: 0.360 AC: 3784 AN: 10522

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19291 AN: 67976

Other (OTH) AF: 0.207 AC: 437 AN: 2112

Alfa AF: 0.267 Hom.: 770

Bravo AF: 0.223

Asia WGS AF: 0.189 AC: 652 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.0
DANN	Benign	0.89
PhyloP100		-0.94

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: rs4713274;

hg19: chr6-29937493;