rs9260952

Positions:

• chr6-29991969-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000688495.1(POLR1HASP):​n.361-14574T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 143,038 control chromosomes in the GnomAD database, including 248 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 0.12 (248 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-14574T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 16862 AN: 142920 Hom.: 247 Cov.: 33

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0845

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.118 AC: 16891 AN: 143038 Hom.: 248 Cov.: 33 AF XY: 0.117 AC XY: 8171 AN XY: 69986

Gnomad4 AFR AF: 0.180

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0845

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0932 Hom.: 78

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.0
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9260952; hg19: chr6-29959746;