rs4959039

Variant names:

• chr6-29989292-A-G
• rs4959039
• ENST00000688495.1:n.361-11897T>C

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-11897T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 140,610 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 0.26 (4578 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171

Genes affected

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-11897T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.261 AC: 36633 AN: 140518 Hom.: 4578 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.294

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.261 AC: 36634 AN: 140610 Hom.: 4578 Cov.: 33 AF XY: 0.261 AC XY: 17939 AN XY: 68862

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.236

Alfa AF: 0.279 Hom.: 747

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4959039; hg19: chr6-29957069;