6-30037977-C-A

Position:

• chr6-30037977-C-A

Variant summary

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

The NR_026751.2(POLR1HASP):​n.443-1994G>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 0.233 in 151,344 control chromosomes in the GnomAD database, including 4,578 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 0.23 (4578 hom., cov: 32)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-1994G>T		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.443-1994G>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+20138G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35282 AN: 151228 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35278 AN: 151344 Hom.: 4578 Cov.: 32 AF XY: 0.234 AC XY: 17297 AN XY: 73952

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.293

Gnomad4 SAS AF: 0.161

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.206

Alfa AF: 0.263 Hom.: 4893

Bravo AF: 0.220

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711207; hg19: chr6-30005754;