rs4959039

Variant names:

• chr6-29989292-A-G
• rs4959039
• ENST00000422224.6:n.823-1065T>C

Variant summary

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

The ENST00000422224.6(POLR1HASP):​n.823-1065T>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 ENST00000422224.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 21 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422224.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000422224.6	TSL:3	n.823-1065T>C		intron	N/A
	POLR1HASP	ENST00000688495.1		n.361-11897T>C		intron	N/A
	POLR1HASP	ENST00000849678.1		n.588+32375T>C		intron	N/A

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

African (AFR) AF: 0.172 AC: 6093 AN: 35402

American (AMR) AF: 0.264 AC: 3685 AN: 13966

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 597 AN: 3152

East Asian (EAS) AF: 0.337 AC: 1580 AN: 4682

South Asian (SAS) AF: 0.182 AC: 783 AN: 4292

European-Finnish (FIN) AF: 0.363 AC: 3807 AN: 10478

Middle Eastern (MID) AF: 0.240 AC: 61 AN: 254

European-Non Finnish (NFE) AF: 0.295 AC: 19307 AN: 65552

Other (OTH) AF: 0.236 AC: 456 AN: 1930

Alfa AF: 0.257 Hom.: 8424

Asia WGS AF: 0.295 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4959039; hg19: chr6-29957069;