rs9261129

chr6-30011802-T-Cchr6-30011802-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_026751.2(POLR1HASP):n.714-9070A>G variant causes a intron, non coding transcript 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 NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.63

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1HASP	NR_026751.2	n.714-9070A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-34407A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.0480

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.192

Alfa AF: 0.134 Hom.: 1444

Bravo AF: 0.191

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	3.4
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261129; hg19: chr6-29979579;