rs6940552

Positions:

• chr6-30044563-G-A

Variant summary

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

The NR_026751.2(POLR1HASP):​n.443-8580C>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 0.118 in 152,142 control chromosomes in the GnomAD database, including 1,506 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 0.12 (1506 hom., cov: 32)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-8580C>T		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.443-8580C>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+13552C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17956 AN: 152026 Hom.: 1497 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.118 AC: 17988 AN: 152142 Hom.: 1506 Cov.: 32 AF XY: 0.117 AC XY: 8666 AN XY: 74374

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0579

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0929 Hom.: 318

Bravo AF: 0.136

Asia WGS AF: 0.144 AC: 500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6940552; hg19: chr6-30012340;