rs16896923

Variant names:

• chr6-30032910-T-C
• rs16896923
• ENST00000420251.5:n.708+1998A>G

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.708+1998A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0629 in 1,025,662 control chromosomes in the GnomAD database, including 2,859 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 0.052 (364 hom., cov: 32)
  • Exomes 𝑓: 0.065 (2495 hom.)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 16 publications found

Genes affected

POLR1HASP (HGNC:):

ETF1P1 (HGNC:3478): (eukaryotic translation termination factor 1 pseudogene 1)

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ETF1P1		n.30032910T>C		intragenic_variant
POLR1HASP	NR_026751.2	n.713+1998A>G		intron_variant	Intron 5 of 5
POLR1HASP	NR_145416.1	n.713+1998A>G		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.708+1998A>G		intron_variant	Intron 5 of 5	1
POLR1HASP	ENST00000437417.5	n.1247+1998A>G		intron_variant	Intron 4 of 5	1
POLR1HASP	ENST00000444051.1	n.108+1998A>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes AF: 0.0523 AC: 7952 AN: 152136 Hom.: 363 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0980

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0556

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0515

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0597

Gnomad OTH AF: 0.0501

GnomAD4 exome AF: 0.0648 AC: 56568 AN: 873408 Hom.: 2495 Cov.: 12 AF XY: 0.0686 AC XY: 31185 AN XY: 454622

African (AFR) AF: 0.0102 AC: 219 AN: 21456

American (AMR) AF: 0.0349 AC: 1230 AN: 35250

Ashkenazi Jewish (ASJ) AF: 0.0569 AC: 1076 AN: 18910

East Asian (EAS) AF: 0.122 AC: 4437 AN: 36466

South Asian (SAS) AF: 0.149 AC: 9887 AN: 66560

European-Finnish (FIN) AF: 0.0489 AC: 2393 AN: 48906

Middle Eastern (MID) AF: 0.0592 AC: 161 AN: 2718

European-Non Finnish (NFE) AF: 0.0573 AC: 34618 AN: 603766

Other (OTH) AF: 0.0647 AC: 2547 AN: 39376

GnomAD4 genome AF: 0.0522 AC: 7950 AN: 152254 Hom.: 364 Cov.: 32 AF XY: 0.0547 AC XY: 4074 AN XY: 74436

African (AFR) AF: 0.0133 AC: 552 AN: 41564

American (AMR) AF: 0.0411 AC: 628 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0556 AC: 193 AN: 3470

East Asian (EAS) AF: 0.190 AC: 985 AN: 5172

South Asian (SAS) AF: 0.160 AC: 771 AN: 4830

European-Finnish (FIN) AF: 0.0515 AC: 545 AN: 10586

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0597 AC: 4064 AN: 68018

Other (OTH) AF: 0.0506 AC: 107 AN: 2116

Alfa AF: 0.0564 Hom.: 745

Bravo AF: 0.0476

Asia WGS AF: 0.158 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	6.4
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs16896923; hg19: chr6-30000687;