rs379221

chr6-29982363-A-G

Variant summary

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

The ENST00000688495.1(POLR1HASP):n.361-4968T>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 0.201 in 151,794 control chromosomes in the GnomAD database, including 2,216 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 0.20 (2216 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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.361-4968T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30506 AN: 151678 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.201 AC: 30552 AN: 151794 Hom.: 2216 Cov.: 33 AF XY: 0.199 AC XY: 14800 AN XY: 74212

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.222

Alfa AF: 0.170 Hom.: 2158

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	2.0
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs379221; hg19: chr6-29950140;