rs6940552

Variant names:

• chr6-30044563-G-A
• rs6940552
• ENST00000420251.5:n.438-8580C>T

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.438-8580C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,142 control chromosomes in the GnomAD database, including 1,506 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 0.12 (1506 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 19 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420251.5. 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
	POLR1HASP	NR_026751.2		n.443-8580C>T		intron	N/A
	POLR1HASP	NR_145416.1		n.443-8580C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.438-8580C>T		intron	N/A
	POLR1HASP	ENST00000437417.5	TSL:1	n.977-8580C>T		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.260-8580C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17956 AN: 152026 Hom.: 1497 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0579

Gnomad OTH AF: 0.132

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.118 AC: 17988 AN: 152142 Hom.: 1506 Cov.: 32 AF XY: 0.117 AC XY: 8666 AN XY: 74374

African (AFR) AF: 0.225 AC: 9313 AN: 41462

American (AMR) AF: 0.142 AC: 2171 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 446 AN: 3470

East Asian (EAS) AF: 0.149 AC: 775 AN: 5186

South Asian (SAS) AF: 0.159 AC: 765 AN: 4816

European-Finnish (FIN) AF: 0.0238 AC: 253 AN: 10610

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.0579 AC: 3937 AN: 67998

Other (OTH) AF: 0.129 AC: 273 AN: 2110

Alfa AF: 0.0907 Hom.: 1681

Bravo AF: 0.136

Asia WGS AF: 0.144 AC: 500 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.9
DANN	Benign	0.51
PhyloP100		0.040
Mutation Taster		=100/0	polymorphism (auto)

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: rs6940552;

hg19: chr6-30012340;