rs3893464

Variant names:

• chr6-29967473-G-A
• rs3893464
• ENST00000849678.1:n.589-20557C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-29967473-G-A
• chr6-29967473-G-C
• chr6-29967473-G-T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-20557C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 151,862 control chromosomes in the GnomAD database, including 16,681 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 0.46 (16681 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 56 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.63 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.589-20557C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+9130C>T		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-10723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70200 AN: 151746 Hom.: 16659 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.463 AC: 70268 AN: 151862 Hom.: 16681 Cov.: 32 AF XY: 0.466 AC XY: 34600 AN XY: 74244

African (AFR) AF: 0.416 AC: 17173 AN: 41292

American (AMR) AF: 0.451 AC: 6894 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3470

East Asian (EAS) AF: 0.626 AC: 3235 AN: 5164

South Asian (SAS) AF: 0.649 AC: 3130 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4797 AN: 10552

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.467 AC: 31765 AN: 67974

Other (OTH) AF: 0.474 AC: 996 AN: 2100

Alfa AF: 0.469 Hom.: 68606

Bravo AF: 0.459

Asia WGS AF: 0.653 AC: 2251 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.0
DANN	Benign	0.63
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: rs3893464;

hg19: chr6-29935250;