rs4713270

Variant names:

• chr6-29966920-G-A
• rs4713270
• ENST00000849678.1:n.589-20004C>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-20004C>T 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 151,836 control chromosomes in the GnomAD database, including 5,646 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 (5646 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 24 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.299 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849678.1	n.589-20004C>T		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+9683C>T		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-10170C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40062 AN: 151720 Hom.: 5645 Cov.: 32

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.264 AC: 40061 AN: 151836 Hom.: 5646 Cov.: 32 AF XY: 0.264 AC XY: 19558 AN XY: 74188

African (AFR) AF: 0.201 AC: 8321 AN: 41298

American (AMR) AF: 0.254 AC: 3886 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3470

East Asian (EAS) AF: 0.311 AC: 1607 AN: 5164

South Asian (SAS) AF: 0.164 AC: 791 AN: 4820

European-Finnish (FIN) AF: 0.363 AC: 3831 AN: 10556

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20136 AN: 67936

Other (OTH) AF: 0.237 AC: 500 AN: 2106

Alfa AF: 0.274 Hom.: 7405

Bravo AF: 0.257

Asia WGS AF: 0.202 AC: 699 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.12
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4713270; hg19: chr6-29934697;