rs6917603

Positions:

• chr6-30049294-T-C

Variant summary

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

The NR_026751.2(POLR1HASP):​n.442+8821A>G 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 0.146 in 152,080 control chromosomes in the GnomAD database, including 2,188 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 0.15 (2188 hom., cov: 31)
• Consequence: POLR1HASP NR_026751.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.43

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POLR1HASP	NR_026751.2	n.442+8821A>G		intron_variant, non_coding_transcript_variant
POLR1HASP	NR_145416.1	n.442+8821A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.360+8821A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22133 AN: 151962 Hom.: 2177 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0318

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0835

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.146 AC: 22177 AN: 152080 Hom.: 2188 Cov.: 31 AF XY: 0.144 AC XY: 10703 AN XY: 74340

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0318

Gnomad4 NFE AF: 0.0835

Gnomad4 OTH AF: 0.164

Alfa AF: 0.127 Hom.: 291

Bravo AF: 0.161

Asia WGS AF: 0.181 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.064
DANN	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6917603; hg19: chr6-30017071;