rs259945

Variant names:

• chr6-30051429-T-A
• rs259945
• ENST00000420251.5:n.437+6686A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-30051429-T-A
• chr6-30051429-T-C

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.437+6686A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 152,234 control chromosomes in the GnomAD database, including 647 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 0.086 (647 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 12 publications found

Genes affected

POLR1HASP (HGNC:):

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420251.5. 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
	POLR1HASP	NR_026751.2		n.442+6686A>T		intron	N/A
	POLR1HASP	NR_145416.1		n.442+6686A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.437+6686A>T		intron	N/A
	POLR1HASP	ENST00000437417.5	TSL:1	n.976+6686A>T		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.259+6686A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13058 AN: 152116 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.0859 AC: 13082 AN: 152234 Hom.: 647 Cov.: 32 AF XY: 0.0863 AC XY: 6421 AN XY: 74434

African (AFR) AF: 0.0638 AC: 2651 AN: 41560

American (AMR) AF: 0.149 AC: 2277 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0669 AC: 232 AN: 3466

East Asian (EAS) AF: 0.0391 AC: 203 AN: 5186

South Asian (SAS) AF: 0.111 AC: 535 AN: 4830

European-Finnish (FIN) AF: 0.0778 AC: 825 AN: 10606

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6111 AN: 67986

Other (OTH) AF: 0.0900 AC: 190 AN: 2110

Alfa AF: 0.0212 Hom.: 15

Bravo AF: 0.0905

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.62
PhyloP100		0.18
Mutation Taster		=100/0	polymorphism (auto)

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: rs259945;

hg19: chr6-30019206;