ENST00000849678.1:n.589-5639A>C

Variant names:

• chr6-29952555-T-G
• rs9260489
• ENST00000849678.1:n.589-5639A>C

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-5639A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 149,500 control chromosomes in the GnomAD database, including 31,438 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 0.65 (31438 hom., cov: 33)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 22 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.731 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849678.1		n.589-5639A>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.66-24009A>C		intron	N/A
	POLR1HASP	ENST00000849682.1		n.751-24009A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 96409 AN: 149384 Hom.: 31383 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.672

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.660

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.646 AC: 96515 AN: 149500 Hom.: 31438 Cov.: 33 AF XY: 0.645 AC XY: 47179 AN XY: 73122

African (AFR) AF: 0.685 AC: 27706 AN: 40476

American (AMR) AF: 0.743 AC: 11099 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2368 AN: 3430

East Asian (EAS) AF: 0.673 AC: 3449 AN: 5124

South Asian (SAS) AF: 0.617 AC: 2941 AN: 4768

European-Finnish (FIN) AF: 0.603 AC: 6347 AN: 10530

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.605 AC: 40540 AN: 66994

Other (OTH) AF: 0.663 AC: 1361 AN: 2054

Alfa AF: 0.496 Hom.: 1261

Bravo AF: 0.662

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs9260489; hg19: chr6-29920332;