6-30036275-C-T

Variant names:

• chr6-30036275-C-T
• rs3869068
• ENST00000420251.5:n.438-292G>A

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.438-292G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,084 control chromosomes in the GnomAD database, including 2,739 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 0.17 (2739 hom., cov: 32)
• Consequence: POLR1HASP ENST00000420251.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.07
• Publications: 35 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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.443-292G>A		intron	N/A
	POLR1HASP	NR_145416.1		n.443-292G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.438-292G>A		intron	N/A
	POLR1HASP	ENST00000437417.5	TSL:1	n.977-292G>A		intron	N/A
	POLR1HASP	ENST00000376797.7	TSL:2	n.260-292G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25883 AN: 151966 Hom.: 2722 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.171 AC: 25935 AN: 152084 Hom.: 2739 Cov.: 32 AF XY: 0.168 AC XY: 12529 AN XY: 74360

African (AFR) AF: 0.274 AC: 11370 AN: 41446

American (AMR) AF: 0.211 AC: 3218 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3472

East Asian (EAS) AF: 0.190 AC: 982 AN: 5178

South Asian (SAS) AF: 0.183 AC: 878 AN: 4810

European-Finnish (FIN) AF: 0.0476 AC: 504 AN: 10590

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7441 AN: 67992

Other (OTH) AF: 0.193 AC: 407 AN: 2108

Alfa AF: 0.141 Hom.: 7178

Bravo AF: 0.191

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.81
DANN	Benign	0.29
PhyloP100		-3.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3869068;

hg19: chr6-30004052;