rs259945

Positions:

• chr6-30051429-T-A
• chr6-30051429-T-C

Variant summary

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

The NR_026751.2(POLR1HASP):​n.442+6686A>T 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 0.0859 in 152,234 control chromosomes in the GnomAD database, including 647 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 0.086 (647 hom., cov: 32)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.442+6686A>T		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.442+6686A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.360+6686A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13058 AN: 152116 Hom.: 645 Cov.: 32

Gnomad AFR AF: 0.0637

Gnomad AMI AF: 0.0419

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.0669

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0778

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0910

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

GnomAD4 genome AF: 0.0859 AC: 13082 AN: 152234 Hom.: 647 Cov.: 32 AF XY: 0.0863 AC XY: 6421 AN XY: 74434

Gnomad4 AFR AF: 0.0638

Gnomad4 AMR AF: 0.149

Gnomad4 ASJ AF: 0.0669

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0778

Gnomad4 NFE AF: 0.0899

Gnomad4 OTH AF: 0.0900

Alfa AF: 0.0212 Hom.: 15

Bravo AF: 0.0905

Asia WGS AF: 0.0710 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259945; hg19: chr6-30019206;