ENST00000849678.1:n.589-3406C>A

Variant names:

• chr6-29950322-G-T
• rs2517713
• ENST00000849678.1:n.589-3406C>A

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-3406C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 150,796 control chromosomes in the GnomAD database, including 32,455 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 0.66 (32455 hom., cov: 31)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 53 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.741 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.589-3406C>A		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.66-21776C>A		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849682.1	n.751-21776C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.655 AC: 98694 AN: 150678 Hom.: 32398 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.582

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.673

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.655 AC: 98802 AN: 150796 Hom.: 32455 Cov.: 31 AF XY: 0.655 AC XY: 48261 AN XY: 73696

African (AFR) AF: 0.705 AC: 28628 AN: 40604

American (AMR) AF: 0.752 AC: 11455 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2399 AN: 3446

East Asian (EAS) AF: 0.686 AC: 3532 AN: 5146

South Asian (SAS) AF: 0.628 AC: 3011 AN: 4798

European-Finnish (FIN) AF: 0.606 AC: 6380 AN: 10530

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.609 AC: 41264 AN: 67752

Other (OTH) AF: 0.674 AC: 1405 AN: 2086

Alfa AF: 0.598 Hom.: 19538

Asia WGS AF: 0.710 AC: 2463 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.33
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs2517713; hg19: chr6-29918099;