rs4713281

Positions:

• chr6-30010575-G-A
• chr6-30010575-G-C

Variant summary

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

The NR_026751.2(POLR1HASP):​n.714-7843C>T 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 0.235 in 150,188 control chromosomes in the GnomAD database, including 4,591 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 0.24 (4591 hom., cov: 32)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POLR1HASP	NR_026751.2	n.714-7843C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-33180C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35303 AN: 150078 Hom.: 4591 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.235 AC: 35299 AN: 150188 Hom.: 4591 Cov.: 32 AF XY: 0.236 AC XY: 17306 AN XY: 73412

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.208

Alfa AF: 0.267 Hom.: 2735

Bravo AF: 0.220

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4713281; hg19: chr6-29978352;