rs9261204

Variant names:

• chr6-30037466-A-G
• rs9261204
• ENST00000420251.5:n.438-1483T>C

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.438-1483T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,182 control chromosomes in the GnomAD database, including 2,726 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 0.17 (2726 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.806
• Publications: 13 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-1483T>C		intron_variant	Intron 3 of 5
POLR1HASP	NR_145416.1	n.443-1483T>C		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.438-1483T>C		intron_variant	Intron 3 of 5	1
POLR1HASP	ENST00000437417.5	n.977-1483T>C		intron_variant	Intron 2 of 5	1
POLR1HASP	ENST00000376797.7	n.260-1483T>C		intron_variant	Intron 2 of 11	2

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25863 AN: 152064 Hom.: 2710 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0477

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.170 AC: 25909 AN: 152182 Hom.: 2726 Cov.: 32 AF XY: 0.168 AC XY: 12530 AN XY: 74402

African (AFR) AF: 0.274 AC: 11374 AN: 41482

American (AMR) AF: 0.210 AC: 3208 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.302 AC: 1049 AN: 3470

East Asian (EAS) AF: 0.185 AC: 960 AN: 5180

South Asian (SAS) AF: 0.183 AC: 881 AN: 4814

European-Finnish (FIN) AF: 0.0477 AC: 507 AN: 10620

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7447 AN: 68004

Other (OTH) AF: 0.189 AC: 399 AN: 2114

Alfa AF: 0.176 Hom.: 1378

Bravo AF: 0.190

Asia WGS AF: 0.180 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.78
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs9261204; hg19: chr6-30005243;