rs9260734

Variant names:

• chr6-29964889-G-A
• rs9260734
• ENST00000849678.1:n.589-17973C>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-17973C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.216 in 151,476 control chromosomes in the GnomAD database, including 3,966 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 0.22 (3966 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.804
• Publications: 32 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=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 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.589-17973C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+11714C>T		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-8139C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32623 AN: 151362 Hom.: 3954 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.216 AC: 32656 AN: 151476 Hom.: 3966 Cov.: 32 AF XY: 0.217 AC XY: 16052 AN XY: 74048

African (AFR) AF: 0.317 AC: 13030 AN: 41068

American (AMR) AF: 0.214 AC: 3259 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1422 AN: 5148

South Asian (SAS) AF: 0.273 AC: 1306 AN: 4776

European-Finnish (FIN) AF: 0.145 AC: 1533 AN: 10580

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10787 AN: 67912

Other (OTH) AF: 0.219 AC: 459 AN: 2100

Alfa AF: 0.181 Hom.: 7643

Bravo AF: 0.227

Asia WGS AF: 0.240 AC: 829 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.51
DANN	Benign	0.75
PhyloP100		-0.80

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: rs9260734;

hg19: chr6-29932666;