6-29987422-G-T

Variant names:

• chr6-29987422-G-T
• rs5025708
• ENST00000688495.1:n.361-10027C>A

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-10027C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,256 control chromosomes in the GnomAD database, including 64,474 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 0.92 (64474 hom., cov: 32)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-10027C>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139792 AN: 152138 Hom.: 64406 Cov.: 32

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.919 AC: 139919 AN: 152256 Hom.: 64474 Cov.: 32 AF XY: 0.920 AC XY: 68456 AN XY: 74432

Gnomad4 AFR AF: 0.974

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.899

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.918

Alfa AF: 0.892 Hom.: 83172

Bravo AF: 0.925

Asia WGS AF: 0.965 AC: 3357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5025708; hg19: chr6-29955199;