rs4947244

chr6-29986587-C-Gchr6-29986587-C-T

Variant summary

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

The ENST00000688495.1(POLR1HASP):n.361-9192G>C 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 0.231 in 151,950 control chromosomes in the GnomAD database, including 4,568 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 0.23 (4568 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-9192G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35131 AN: 151834 Hom.: 4568 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.231 AC: 35126 AN: 151950 Hom.: 4568 Cov.: 33 AF XY: 0.232 AC XY: 17206 AN XY: 74260

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.203

Alfa AF: 0.178 Hom.: 470

Bravo AF: 0.220

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.3
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4947244; hg19: chr6-29954364;