chr6-30035016-G-C

Variant names:

• chr6-30035016-G-C
• rs3121593
• ENST00000420251.5:n.600C>G

Variant summary

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

The ENST00000420251.5(POLR1HASP):​n.600C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,276 control chromosomes in the GnomAD database, including 60,889 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 0.89 (60865 hom., cov: 31)
  • Exomes 𝑓: 0.85 (24 hom.)
• Consequence: POLR1HASP ENST00000420251.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 13 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	NR_026751.2		n.605C>G		non_coding_transcript_exon	Exon 5 of 6
	POLR1HASP	NR_145416.1		n.605C>G		non_coding_transcript_exon	Exon 5 of 7

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000420251.5	TSL:1	n.600C>G		non_coding_transcript_exon	Exon 5 of 6
	POLR1HASP	ENST00000437417.5	TSL:1	n.1139C>G		non_coding_transcript_exon	Exon 4 of 6
	POLR1HASP	ENST00000376797.7	TSL:2	n.422C>G		non_coding_transcript_exon	Exon 4 of 12

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135896 AN: 152090 Hom.: 60803 Cov.: 31

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.907

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.889

GnomAD4 exome AF: 0.853 AC: 58 AN: 68 Hom.: 24 Cov.: 0 AF XY: 0.820 AC XY: 41 AN XY: 50

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.889 AC: 16 AN: 18

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.864 AC: 38 AN: 44

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.894 AC: 136016 AN: 152208 Hom.: 60865 Cov.: 31 AF XY: 0.895 AC XY: 66599 AN XY: 74416

African (AFR) AF: 0.902 AC: 37450 AN: 41502

American (AMR) AF: 0.914 AC: 13984 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.907 AC: 3149 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5108 AN: 5176

South Asian (SAS) AF: 0.945 AC: 4563 AN: 4828

European-Finnish (FIN) AF: 0.891 AC: 9437 AN: 10596

Middle Eastern (MID) AF: 0.911 AC: 266 AN: 292

European-Non Finnish (NFE) AF: 0.872 AC: 59319 AN: 68012

Other (OTH) AF: 0.890 AC: 1879 AN: 2112

Alfa AF: 0.882 Hom.: 28382

Bravo AF: 0.897

Asia WGS AF: 0.958 AC: 3332 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	1.2
DANN	Benign	0.50
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs3121593; hg19: chr6-30002793;