chr6-30041219-C-T

Position:

• chr6-30041219-C-T

Variant summary

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

The NR_026751.2(POLR1HASP):​n.443-5236G>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 0.899 in 152,244 control chromosomes in the GnomAD database, including 61,590 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 0.90 (61590 hom., cov: 31)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-5236G>A		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.443-5236G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.360+16896G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136687 AN: 152126 Hom.: 61527 Cov.: 31

Gnomad AFR AF: 0.919

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.917

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.899 AC: 136809 AN: 152244 Hom.: 61590 Cov.: 31 AF XY: 0.900 AC XY: 66967 AN XY: 74440

Gnomad4 AFR AF: 0.919

Gnomad4 AMR AF: 0.917

Gnomad4 ASJ AF: 0.907

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.945

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.895

Alfa AF: 0.880 Hom.: 21712

Bravo AF: 0.903

Asia WGS AF: 0.961 AC: 3341 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	0.51
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9261212; hg19: chr6-30008996;