chr6-30057726-G-A

Position:

• chr6-30057726-G-A

Variant summary

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

The ENST00000700857.1(POLR1HASP):​n.905C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 197,588 control chromosomes in the GnomAD database, including 7,464 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 0.26 (5517 hom., cov: 32)
  • Exomes 𝑓: 0.28 (1947 hom.)
• Consequence: POLR1HASP ENST00000700857.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.442+389C>T		intron_variant
POLR1HASP	NR_145416.1	n.442+389C>T		intron_variant
POLR1HASP	NR_145417.1	n.442-9C>T		intron_variant
POLR1HASP	NR_145418.1	n.188-9C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.437+389C>T		intron_variant		1
POLR1HASP	ENST00000431012.5	n.178-9C>T		intron_variant		1
POLR1HASP	ENST00000437417.5	n.976+389C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38823 AN: 151916 Hom.: 5507 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.226

GnomAD4 exome AF: 0.279 AC: 12701 AN: 45554 Hom.: 1947 Cov.: 0 AF XY: 0.280 AC XY: 6920 AN XY: 24692

Gnomad4 AFR exome AF: 0.137

Gnomad4 AMR exome AF: 0.208

Gnomad4 ASJ exome AF: 0.233

Gnomad4 EAS exome AF: 0.256

Gnomad4 SAS exome AF: 0.261

Gnomad4 FIN exome AF: 0.329

Gnomad4 NFE exome AF: 0.295

Gnomad4 OTH exome AF: 0.279

GnomAD4 genome AF: 0.256 AC: 38845 AN: 152034 Hom.: 5517 Cov.: 32 AF XY: 0.257 AC XY: 19092 AN XY: 74304

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.232

Alfa AF: 0.307 Hom.: 13788

Bravo AF: 0.241

Asia WGS AF: 0.316 AC: 1101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	19
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259919; hg19: chr6-30025503;