Variant rs16896944 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000637794.1(POLR1HASP):n.244A>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,674 control chromosomes in the GnomAD database, including 772 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 0.070 ( 772 hom., cov: 32)

Exomes 𝑓: 0.011 ( 0 hom. )

Consequence

POLR1HASP
ENST00000637794.1 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.42

Variant links:

Genes affected

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

POLR1HASP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.25).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.176 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
POLR1HASP	NR_026751.2 linkuse as main transcript	n.367-179A>G	intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145417.1 linkuse as main transcript	n.364A>G	splice_region_variant, non_coding_transcript_exon_variant	1/3
POLR1HASP	NR_145416.1 linkuse as main transcript	n.367-179A>G	intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145418.1 linkuse as main transcript	n.112-179A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000637794.1 linkuse as main transcript	n.244A>G		splice_region_variant, non_coding_transcript_exon_variant	1/3
POLR1HASP	ENST00000688495.1 linkuse as main transcript	n.285-179A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0704

AC:

10705

AN:

152120

Hom.:

772

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0554

Gnomad ASJ

AF:

0.0436

Gnomad EAS

AF:

0.00211

Gnomad SAS

AF:

0.0120

Gnomad FIN

AF:

0.00264

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0291

Gnomad OTH

AF:

0.0813

GnomAD4 exome

AF:

0.0115

AC:

AN:

436

Hom.:

Cov.:

AF XY:

0.0152

AC XY:

AN XY:

264

show subpopulations

Gnomad4 FIN exome

AF:

0.00935

Gnomad4 NFE exome

AF:

0.250

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

AF:

0.0704

AC:

10711

AN:

152238

Hom.:

772

Cov.:

AF XY:

0.0671

AC XY:

4998

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.179

Gnomad4 AMR

AF:

0.0553

Gnomad4 ASJ

AF:

0.0436

Gnomad4 EAS

AF:

0.00212

Gnomad4 SAS

AF:

0.0118

Gnomad4 FIN

AF:

0.00264

Gnomad4 NFE

AF:

0.0291

Gnomad4 OTH

AF:

0.0800

Alfa

AF:

0.0377

Hom.:

265

Bravo

AF:

0.0807

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.25

CADD

Benign

DANN

Benign

0.76

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over