chr6-30049294-T-C

Variant names:

• chr6-30049294-T-C
• rs6917603
• ENST00000420251.5:n.437+8821A>G

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.437+8821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,080 control chromosomes in the GnomAD database, including 2,188 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 0.15 (2188 hom., cov: 31)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43
• Publications: 22 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000420251.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	NR_026751.2		n.442+8821A>G		intron	N/A
	POLR1HASP	NR_145416.1		n.442+8821A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.437+8821A>G		intron	N/A
	POLR1HASP	ENST00000437417.5	TSL:1	n.976+8821A>G		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.259+8821A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22133 AN: 151962 Hom.: 2177 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.146 AC: 22177 AN: 152080 Hom.: 2188 Cov.: 31 AF XY: 0.144 AC XY: 10703 AN XY: 74340

African (AFR) AF: 0.267 AC: 11059 AN: 41424

American (AMR) AF: 0.141 AC: 2150 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 954 AN: 3472

East Asian (EAS) AF: 0.158 AC: 816 AN: 5170

South Asian (SAS) AF: 0.159 AC: 766 AN: 4830

European-Finnish (FIN) AF: 0.0318 AC: 337 AN: 10594

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.0835 AC: 5675 AN: 67986

Other (OTH) AF: 0.164 AC: 346 AN: 2110

Alfa AF: 0.252 Hom.: 1428

Bravo AF: 0.161

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.064
DANN	Benign	0.15
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6917603; hg19: chr6-30017071;