6-29987422-G-T

Position:

• chr6-29987422-G-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-10027C>A		intron_variant, non_coding_transcript_variant

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;