rs2256543

Variant names:

• chr6-29970056-T-C
• rs2256543
• ENST00000849678.1:n.589-23140A>G

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-23140A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,194 control chromosomes in the GnomAD database, including 27,132 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 0.60 (27132 hom., cov: 29)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 35 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 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.589-23140A>G		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+6547A>G		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-13306A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90000 AN: 151086 Hom.: 27084 Cov.: 29

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.596 AC: 90087 AN: 151194 Hom.: 27132 Cov.: 29 AF XY: 0.598 AC XY: 44157 AN XY: 73898

African (AFR) AF: 0.611 AC: 24965 AN: 40830

American (AMR) AF: 0.637 AC: 9691 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3470

East Asian (EAS) AF: 0.743 AC: 3825 AN: 5146

South Asian (SAS) AF: 0.640 AC: 3081 AN: 4814

European-Finnish (FIN) AF: 0.562 AC: 5905 AN: 10516

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38501 AN: 67906

Other (OTH) AF: 0.598 AC: 1253 AN: 2094

Alfa AF: 0.578 Hom.: 76931

Bravo AF: 0.603

Asia WGS AF: 0.607 AC: 2090 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
DANN	Benign	0.35
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs2256543; hg19: chr6-29937833;