ENST00000849679.1:n.493+15632G>A

Variant names:

• chr6-29911752-C-T
• rs2524024
• ENST00000849679.1:n.493+15632G>A

Variant summary

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

The ENST00000849679.1(POLR1HASP):​n.493+15632G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 145,858 control chromosomes in the GnomAD database, including 55,927 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 0.86 (55927 hom., cov: 28)
• Consequence: POLR1HASP ENST00000849679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 10 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849679.1. 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	ENST00000849679.1		n.493+15632G>A		intron	N/A
	POLR1HASP	ENST00000849682.1		n.1075-10801G>A		intron	N/A
	POLR1HASP	ENST00000849693.1		n.1100-21767G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.860 AC: 125384 AN: 145752 Hom.: 55870 Cov.: 28

Gnomad AFR AF: 0.905

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.920

Gnomad FIN AF: 0.694

Gnomad MID AF: 0.897

Gnomad NFE AF: 0.836

Gnomad OTH AF: 0.878

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

GnomAD4 genome AF: 0.860 AC: 125494 AN: 145858 Hom.: 55927 Cov.: 28 AF XY: 0.856 AC XY: 60834 AN XY: 71056

African (AFR) AF: 0.905 AC: 35672 AN: 39414

American (AMR) AF: 0.900 AC: 12829 AN: 14250

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3022 AN: 3386

East Asian (EAS) AF: 0.983 AC: 4617 AN: 4698

South Asian (SAS) AF: 0.921 AC: 4070 AN: 4418

European-Finnish (FIN) AF: 0.694 AC: 7027 AN: 10120

Middle Eastern (MID) AF: 0.893 AC: 241 AN: 270

European-Non Finnish (NFE) AF: 0.836 AC: 55521 AN: 66416

Other (OTH) AF: 0.878 AC: 1762 AN: 2006

Alfa AF: 0.876 Hom.: 31395

Asia WGS AF: 0.947 AC: 2947 AN: 3112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs2524024; hg19: chr6-29879529;