rs7758512

Positions:

• chr6-30002812-T-G

Variant summary

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

The NR_026751.2(POLR1HASP):​n.714-80A>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 0.171 in 152,414 control chromosomes in the GnomAD database, including 2,744 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 0.17 (2742 hom., cov: 32)
  • Exomes 𝑓: 0.16 (2 hom.)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.714-80A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-25417A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25911 AN: 152032 Hom.: 2725 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.0475

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.193

GnomAD4 exome AF: 0.163 AC: 43 AN: 264 Hom.: 2 AF XY: 0.149 AC XY: 25 AN XY: 168

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.125

Gnomad4 SAS exome AF: 0.0714

Gnomad4 FIN exome AF: 0.133

Gnomad4 NFE exome AF: 0.148

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.171 AC: 25963 AN: 152150 Hom.: 2742 Cov.: 32 AF XY: 0.169 AC XY: 12554 AN XY: 74412

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0475

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.193

Alfa AF: 0.134 Hom.: 1830

Bravo AF: 0.191

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7758512; hg19: chr6-29970589;