rs379221

Variant names:

• chr6-29982363-A-G
• rs379221
• ENST00000688495.1:n.361-4968T>C

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-4968T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,794 control chromosomes in the GnomAD database, including 2,216 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 0.20 (2216 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 17 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.268 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.361-4968T>C		intron_variant	Intron 3 of 3
POLR1HASP	ENST00000849678.1	n.589-35447T>C		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849680.1	n.506-25613T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30506 AN: 151678 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.201 AC: 30552 AN: 151794 Hom.: 2216 Cov.: 33 AF XY: 0.199 AC XY: 14800 AN XY: 74212

African (AFR) AF: 0.272 AC: 11219 AN: 41266

American (AMR) AF: 0.251 AC: 3822 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 669 AN: 3466

East Asian (EAS) AF: 0.154 AC: 795 AN: 5176

South Asian (SAS) AF: 0.235 AC: 1128 AN: 4804

European-Finnish (FIN) AF: 0.125 AC: 1330 AN: 10604

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.161 AC: 10954 AN: 67942

Other (OTH) AF: 0.222 AC: 468 AN: 2106

Alfa AF: 0.180 Hom.: 4795

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.75
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs379221; hg19: chr6-29950140;