rs7219550

Variant names:

• chr17-7498352-G-A
• rs7219550
• ENST00000674977.2:c.1335+142G>A

Variant summary

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

The NM_000937.5(POLR2A):​c.1335+142G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 868,092 control chromosomes in the GnomAD database, including 14,723 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 0.17 (2493 hom., cov: 33)
  • Exomes 𝑓: 0.18 (12230 hom.)
• Consequence: POLR2A NM_000937.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164

Genes affected

POLR2A (HGNC:9187): (RNA polymerase II subunit A) This gene encodes the largest subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains a carboxy terminal domain composed of heptapeptide repeats that are essential for polymerase activity. These repeats contain serine and threonine residues that are phosphorylated in actively transcribing RNA polymerase. In addition, this subunit, in combination with several other polymerase subunits, forms the DNA binding domain of the polymerase, a groove in which the DNA template is transcribed into RNA. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR2A	NM_000937.5	c.1335+142G>A		intron_variant	Intron 8 of 29		NP_000928.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR2A	ENST00000674977.2	c.1335+142G>A		intron_variant	Intron 8 of 29			ENSP00000502190.2
POLR2A	ENST00000572844.1	n.1480+142G>A		intron_variant	Intron 8 of 9	1
POLR2A	ENST00000617998.6	n.1734+142G>A		intron_variant	Intron 8 of 28	1
POLR2A	ENST00000576952.1	n.365G>A		non_coding_transcript_exon_variant	Exon 2 of 2	2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25743 AN: 152108 Hom.: 2480 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.175 AC: 125452 AN: 715866 Hom.: 12230 Cov.: 9 AF XY: 0.176 AC XY: 64516 AN XY: 367218

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.229

Gnomad4 ASJ exome AF: 0.0976

Gnomad4 EAS exome AF: 0.220

Gnomad4 SAS exome AF: 0.218

Gnomad4 FIN exome AF: 0.304

Gnomad4 NFE exome AF: 0.162

Gnomad4 OTH exome AF: 0.170

GnomAD4 genome AF: 0.169 AC: 25767 AN: 152226 Hom.: 2493 Cov.: 33 AF XY: 0.178 AC XY: 13227 AN XY: 74420

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.158

Alfa AF: 0.162 Hom.: 3075

Bravo AF: 0.157

Asia WGS AF: 0.275 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.5
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219550; hg19: chr17-7401671;