6-30011802-T-C

Variant names:

• chr6-30011802-T-C
• rs9261129
• ENST00000420251.5:n.709-9070A>G

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.709-9070A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 151,766 control chromosomes in the GnomAD database, including 2,727 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 (2727 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63
• Publications: 25 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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.714-9070A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.709-9070A>G		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.626-1971A>G		intron	N/A
	POLR1HASP	ENST00000422224.6	TSL:3	n.822+9865A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25867 AN: 151648 Hom.: 2710 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0480

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.171 AC: 25919 AN: 151766 Hom.: 2727 Cov.: 32 AF XY: 0.169 AC XY: 12517 AN XY: 74150

African (AFR) AF: 0.275 AC: 11353 AN: 41332

American (AMR) AF: 0.211 AC: 3218 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1050 AN: 3464

East Asian (EAS) AF: 0.190 AC: 979 AN: 5154

South Asian (SAS) AF: 0.183 AC: 880 AN: 4818

European-Finnish (FIN) AF: 0.0480 AC: 505 AN: 10530

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.110 AC: 7445 AN: 67884

Other (OTH) AF: 0.192 AC: 405 AN: 2110

Alfa AF: 0.152 Hom.: 3040

Bravo AF: 0.191

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs9261129; hg19: chr6-29979579;