ENST00000849678.1:n.589-5843C>A

Variant names:

• chr6-29952759-G-T
• rs2975042
• ENST00000849678.1:n.589-5843C>A

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-5843C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 151,372 control chromosomes in the GnomAD database, including 32,287 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 (32287 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.633
• Publications: 20 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.738 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.589-5843C>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+23844C>A		intron	N/A
	POLR1HASP	ENST00000849682.1		n.750+23844C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98309 AN: 151254 Hom.: 32230 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.749

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.602

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.650 AC: 98417 AN: 151372 Hom.: 32287 Cov.: 32 AF XY: 0.650 AC XY: 48052 AN XY: 73952

African (AFR) AF: 0.694 AC: 28475 AN: 41016

American (AMR) AF: 0.749 AC: 11427 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2392 AN: 3456

East Asian (EAS) AF: 0.681 AC: 3521 AN: 5168

South Asian (SAS) AF: 0.623 AC: 3004 AN: 4820

European-Finnish (FIN) AF: 0.602 AC: 6318 AN: 10494

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41159 AN: 67856

Other (OTH) AF: 0.664 AC: 1396 AN: 2102

Alfa AF: 0.561 Hom.: 2206

Bravo AF: 0.665

Asia WGS AF: 0.704 AC: 2426 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.42
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2975042; hg19: chr6-29920536;