ENST00000849678.1:n.589-12402C>T

Variant names:

• chr6-29959318-G-A
• rs2735085
• ENST00000849678.1:n.589-12402C>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-12402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,964 control chromosomes in the GnomAD database, including 3,963 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 0.22 (3963 hom., cov: 33)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.909
• Publications: 10 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 (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849678.1	n.589-12402C>T		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+17285C>T		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-2568C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33242 AN: 151848 Hom.: 3945 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.219 AC: 33287 AN: 151964 Hom.: 3963 Cov.: 33 AF XY: 0.220 AC XY: 16328 AN XY: 74276

African (AFR) AF: 0.277 AC: 11443 AN: 41362

American (AMR) AF: 0.246 AC: 3754 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.217 AC: 750 AN: 3464

East Asian (EAS) AF: 0.266 AC: 1375 AN: 5176

South Asian (SAS) AF: 0.271 AC: 1308 AN: 4824

European-Finnish (FIN) AF: 0.150 AC: 1586 AN: 10570

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12329 AN: 67988

Other (OTH) AF: 0.232 AC: 489 AN: 2108

Alfa AF: 0.195 Hom.: 6550

Asia WGS AF: 0.234 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.54
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs2735085; hg19: chr6-29927095;