rs3869062

Variant names:

• chr6-29967114-A-G
• rs3869062
• ENST00000849678.1:n.589-20198T>C

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-20198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 143,480 control chromosomes in the GnomAD database, including 454 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 0.058 (454 hom., cov: 33)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.131
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.252 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.589-20198T>C		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+9489T>C		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-10364T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8305 AN: 143364 Hom.: 452 Cov.: 33

Gnomad AFR AF: 0.0137

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0572

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.0587

Gnomad MID AF: 0.0574

Gnomad NFE AF: 0.0639

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0579 AC: 8305 AN: 143480 Hom.: 454 Cov.: 33 AF XY: 0.0612 AC XY: 4287 AN XY: 70070

African (AFR) AF: 0.0137 AC: 546 AN: 39864

American (AMR) AF: 0.0471 AC: 678 AN: 14406

Ashkenazi Jewish (ASJ) AF: 0.0572 AC: 194 AN: 3394

East Asian (EAS) AF: 0.264 AC: 1267 AN: 4804

South Asian (SAS) AF: 0.164 AC: 768 AN: 4682

European-Finnish (FIN) AF: 0.0587 AC: 554 AN: 9440

Middle Eastern (MID) AF: 0.0580 AC: 16 AN: 276

European-Non Finnish (NFE) AF: 0.0639 AC: 4077 AN: 63782

Other (OTH) AF: 0.0585 AC: 116 AN: 1984

Alfa AF: 0.0559 Hom.: 234

Bravo AF: 0.0508

Asia WGS AF: 0.162 AC: 556 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.0
DANN	Benign	0.50
PhyloP100		0.13

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: rs3869062;

hg19: chr6-29934891;