6-29964515-G-T

Variant names:

• chr6-29964515-G-T
• rs2523933
• ENST00000849678.1:n.589-17599C>A

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-17599C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,970 control chromosomes in the GnomAD database, including 5,776 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 0.27 (5776 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• 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=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.293 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.589-17599C>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+12088C>A		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-7765C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40935 AN: 151856 Hom.: 5767 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.269 AC: 40945 AN: 151970 Hom.: 5776 Cov.: 32 AF XY: 0.270 AC XY: 20085 AN XY: 74310

African (AFR) AF: 0.214 AC: 8838 AN: 41352

American (AMR) AF: 0.250 AC: 3826 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 894 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1267 AN: 5172

South Asian (SAS) AF: 0.300 AC: 1451 AN: 4830

European-Finnish (FIN) AF: 0.328 AC: 3471 AN: 10578

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20170 AN: 67978

Other (OTH) AF: 0.265 AC: 559 AN: 2106

Alfa AF: 0.266 Hom.: 5346

Bravo AF: 0.259

Asia WGS AF: 0.343 AC: 1184 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		1.0

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: rs2523933;

hg19: chr6-29932292;