rs4947244

Variant names:

• chr6-29986587-C-G
• rs4947244
• ENST00000688495.1:n.361-9192G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-29986587-C-G
• chr6-29986587-C-T

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-9192G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 151,950 control chromosomes in the GnomAD database, including 4,568 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 (4568 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.482
• Publications: 28 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688495.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000688495.1		n.361-9192G>C		intron	N/A
	POLR1HASP	ENST00000849678.1		n.588+35080G>C		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-29837G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35131 AN: 151834 Hom.: 4568 Cov.: 33

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.231 AC: 35126 AN: 151950 Hom.: 4568 Cov.: 33 AF XY: 0.232 AC XY: 17206 AN XY: 74260

African (AFR) AF: 0.127 AC: 5261 AN: 41476

American (AMR) AF: 0.229 AC: 3500 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3472

East Asian (EAS) AF: 0.294 AC: 1513 AN: 5152

South Asian (SAS) AF: 0.149 AC: 718 AN: 4810

European-Finnish (FIN) AF: 0.359 AC: 3774 AN: 10524

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

European-Non Finnish (NFE) AF: 0.280 AC: 19035 AN: 67944

Other (OTH) AF: 0.203 AC: 429 AN: 2110

Alfa AF: 0.178 Hom.: 470

Bravo AF: 0.220

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs4947244; hg19: chr6-29954364;