rs60131261

Variant names:

• chr6-29969558-GTTTA-G
• rs60131261
• ENST00000849678.1:n.589-22646_589-22643delTAAA

Your query was ambiguous. Multiple possible variants found:

• chr6-29969558-GTTTA-G
• chr6-29969558-GTTTA-GTTTATTTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000849678.1(POLR1HASP):​n.589-22646_589-22643delTAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5607 hom., cov: 20)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.237
• Publications: 9 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 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.589-22646_589-22643delTAAA		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+7041_65+7044delTAAA		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-12812_506-12809delTAAA		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40200 AN: 151460 Hom.: 5607 Cov.: 20

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.215

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: 0.265 AC: 40197 AN: 151574 Hom.: 5607 Cov.: 20 AF XY: 0.264 AC XY: 19579 AN XY: 74024

African (AFR) AF: 0.208 AC: 8599 AN: 41302

American (AMR) AF: 0.256 AC: 3900 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3468

East Asian (EAS) AF: 0.310 AC: 1595 AN: 5148

South Asian (SAS) AF: 0.165 AC: 786 AN: 4766

European-Finnish (FIN) AF: 0.359 AC: 3763 AN: 10472

Middle Eastern (MID) AF: 0.207 AC: 60 AN: 290

European-Non Finnish (NFE) AF: 0.296 AC: 20074 AN: 67890

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

Alfa AF: 0.290 Hom.: 816

Bravo AF: 0.260

Asia WGS AF: 0.203 AC: 701 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.24

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: rs60131261; hg19: chr6-29937335;