6-30058369-T-G

Variant names:

• chr6-30058369-T-G
• rs16896944
• ENST00000452229.2:n.364A>C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000452229.2(POLR1HASP):​n.364A>C variant causes a splice region, 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: 32)
• Consequence: POLR1HASP ENST00000452229.2 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.42

Genes affected

POLR1HASP (HGNC:13924): (POLR1H antisense, pseudogene)

ENSG00000275856 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POLR1HASP	NR_145417.1	n.364A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 3
POLR1HASP	NR_026751.2	n.367-179A>C		intron_variant	Intron 2 of 5
POLR1HASP	NR_145416.1	n.367-179A>C		intron_variant	Intron 2 of 6
POLR1HASP	NR_145418.1	n.112-179A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000452229.2	n.364A>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 3	1
POLR1HASP	ENST00000420251.5	n.362-179A>C		intron_variant	Intron 2 of 5	1
POLR1HASP	ENST00000431012.5	n.102-179A>C		intron_variant	Intron 1 of 2	1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	15
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16896944; hg19: chr6-30026146;