rs4711207

Variant names:

• chr6-30037977-C-A
• rs4711207
• ENST00000420251.5:n.438-1994G>T

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.438-1994G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,344 control chromosomes in the GnomAD database, including 4,578 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 0.23 (4578 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290
• Publications: 28 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.443-1994G>T		intron_variant	Intron 3 of 5
POLR1HASP	NR_145416.1	n.443-1994G>T		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000420251.5	n.438-1994G>T		intron_variant	Intron 3 of 5	1
POLR1HASP	ENST00000437417.5	n.977-1994G>T		intron_variant	Intron 2 of 5	1
POLR1HASP	ENST00000376797.7	n.260-1994G>T		intron_variant	Intron 2 of 11	2

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35282 AN: 151228 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.233 AC: 35278 AN: 151344 Hom.: 4578 Cov.: 32 AF XY: 0.234 AC XY: 17297 AN XY: 73952

African (AFR) AF: 0.128 AC: 5294 AN: 41312

American (AMR) AF: 0.233 AC: 3530 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 575 AN: 3366

East Asian (EAS) AF: 0.293 AC: 1511 AN: 5150

South Asian (SAS) AF: 0.161 AC: 775 AN: 4800

European-Finnish (FIN) AF: 0.359 AC: 3777 AN: 10520

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19059 AN: 67720

Other (OTH) AF: 0.206 AC: 434 AN: 2102

Alfa AF: 0.259 Hom.: 8409

Bravo AF: 0.220

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.65
PhyloP100		-0.029

Splicing

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

Other links and lift over

dbSNP: rs4711207; hg19: chr6-30005754;