rs3121593

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-30035016-G-A
• chr6-30035016-G-C
• chr6-30035016-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000420251.5(POLR1HASP):​n.600C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

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>T		non_coding_transcript_exon	Exon 5 of 6
	POLR1HASP	NR_145416.1		n.605C>T		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>T		non_coding_transcript_exon	Exon 5 of 6
	POLR1HASP	ENST00000437417.5	TSL:1	n.1139C>T		non_coding_transcript_exon	Exon 4 of 6
	POLR1HASP	ENST00000376797.7	TSL:2	n.422C>T		non_coding_transcript_exon	Exon 4 of 12

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.46
PhyloP100		-0.69
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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;