6-30056900-C-T

Variant names:

• chr6-30056900-C-T
• rs9366752
• ENST00000431012.5:n.995G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000431012.5(POLR1HASP):​n.995G>A 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 0.224 in 367,720 control chromosomes in the GnomAD database, including 10,063 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 0.21 (3736 hom., cov: 32)
  • Exomes 𝑓: 0.23 (6327 hom.)
• Consequence: POLR1HASP ENST00000431012.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907
• Publications: 23 publications found

Genes affected

POLR1HASP (HGNC:):

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_145417.1	n.1259G>A		non_coding_transcript_exon_variant	Exon 3 of 3
POLR1HASP	NR_145418.1	n.1005G>A		non_coding_transcript_exon_variant	Exon 3 of 3
POLR1HASP	NR_026751.2	n.442+1215G>A		intron_variant	Intron 3 of 5
POLR1HASP	NR_145416.1	n.442+1215G>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000431012.5	n.995G>A		non_coding_transcript_exon_variant	Exon 3 of 3	1
POLR1HASP	ENST00000420251.5	n.437+1215G>A		intron_variant	Intron 3 of 5	1
POLR1HASP	ENST00000437417.5	n.976+1215G>A		intron_variant	Intron 2 of 5	1

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32063 AN: 150722 Hom.: 3736 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.232 AC: 50250 AN: 216884 Hom.: 6327 Cov.: 0 AF XY: 0.222 AC XY: 26962 AN XY: 121472

African (AFR) AF: 0.122 AC: 677 AN: 5552

American (AMR) AF: 0.268 AC: 3295 AN: 12288

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 802 AN: 4942

East Asian (EAS) AF: 0.309 AC: 2681 AN: 8676

South Asian (SAS) AF: 0.163 AC: 6996 AN: 43048

European-Finnish (FIN) AF: 0.330 AC: 3079 AN: 9318

Middle Eastern (MID) AF: 0.167 AC: 137 AN: 818

European-Non Finnish (NFE) AF: 0.248 AC: 30247 AN: 121794

Other (OTH) AF: 0.224 AC: 2336 AN: 10448

GnomAD4 genome AF: 0.213 AC: 32061 AN: 150836 Hom.: 3736 Cov.: 32 AF XY: 0.216 AC XY: 15883 AN XY: 73644

African (AFR) AF: 0.124 AC: 5098 AN: 41040

American (AMR) AF: 0.226 AC: 3430 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 555 AN: 3428

East Asian (EAS) AF: 0.296 AC: 1518 AN: 5136

South Asian (SAS) AF: 0.161 AC: 773 AN: 4788

European-Finnish (FIN) AF: 0.352 AC: 3640 AN: 10332

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.242 AC: 16354 AN: 67656

Other (OTH) AF: 0.197 AC: 414 AN: 2104

Alfa AF: 0.228 Hom.: 10455

Bravo AF: 0.200

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.87
DANN	Benign	0.58
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9366752; hg19: chr6-30024677; COSMIC: COSV107404924;