ENST00000844107.1:n.211-4901G>A

Variant names:

• chr13-48134675-C-T
• rs9568011
• ENST00000844107.1:n.211-4901G>A

Variant summary

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

The ENST00000844107.1(ENSG00000309815):​n.211-4901G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0846 in 163,902 control chromosomes in the GnomAD database, including 816 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 0.086 (776 hom., cov: 32)
  • Exomes 𝑓: 0.072 (40 hom.)
• Consequence: ENSG00000309815 ENST00000844107.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 2 publications found

Genes affected

ENSG00000309815 (HGNC:):

POLR2KP2 (HGNC:42652): (RNA polymerase II subunit K pseudogene 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844107.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309815	ENST00000844107.1		n.211-4901G>A		intron	N/A
	POLR2KP2	ENST00000438155.2	TSL:6	n.-141G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13025 AN: 152066 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.0235

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0842

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0690

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.113

GnomAD4 exome AF: 0.0716 AC: 839 AN: 11718 Hom.: 40 AF XY: 0.0699 AC XY: 395 AN XY: 5654

African (AFR) AF: 0.333 AC: 2 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 8

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.0713 AC: 822 AN: 11526

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.100 AC: 9 AN: 90

Other (OTH) AF: 0.0658 AC: 5 AN: 76

GnomAD4 genome AF: 0.0856 AC: 13025 AN: 152184 Hom.: 776 Cov.: 32 AF XY: 0.0851 AC XY: 6330 AN XY: 74416

African (AFR) AF: 0.0234 AC: 973 AN: 41532

American (AMR) AF: 0.0841 AC: 1284 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 812 AN: 3472

East Asian (EAS) AF: 0.0156 AC: 81 AN: 5184

South Asian (SAS) AF: 0.186 AC: 895 AN: 4820

European-Finnish (FIN) AF: 0.0690 AC: 731 AN: 10594

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7908 AN: 67988

Other (OTH) AF: 0.114 AC: 242 AN: 2114

Alfa AF: 0.106 Hom.: 637

Bravo AF: 0.0815

Asia WGS AF: 0.121 AC: 420 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.37
PhyloP100		-0.27

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9568011;

hg19: chr13-48708811;