6-29952349-C-T

Variant names:

• chr6-29952349-C-T
• rs9260475
• ENST00000849678.1:n.589-5433G>A

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-5433G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 148,600 control chromosomes in the GnomAD database, including 22,300 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 0.55 (22300 hom., cov: 33)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.613
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.628 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.589-5433G>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.66-23803G>A		intron	N/A
	POLR1HASP	ENST00000849682.1		n.751-23803G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.554 AC: 82257 AN: 148480 Hom.: 22278 Cov.: 33

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.554 AC: 82324 AN: 148600 Hom.: 22300 Cov.: 33 AF XY: 0.556 AC XY: 40405 AN XY: 72684

African (AFR) AF: 0.552 AC: 22070 AN: 39994

American (AMR) AF: 0.639 AC: 9369 AN: 14662

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2017 AN: 3372

East Asian (EAS) AF: 0.634 AC: 3204 AN: 5056

South Asian (SAS) AF: 0.548 AC: 2576 AN: 4704

European-Finnish (FIN) AF: 0.553 AC: 5808 AN: 10504

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.530 AC: 35528 AN: 67054

Other (OTH) AF: 0.555 AC: 1142 AN: 2056

Alfa AF: 0.552 Hom.: 2395

Bravo AF: 0.570

Asia WGS AF: 0.632 AC: 2195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.69
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs9260475; hg19: chr6-29920126;