rs3901554

Positions:

• chr6-29987248-T-C

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-9853A>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 0.0527 in 152,208 control chromosomes in the GnomAD database, including 259 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 0.053 (259 hom., cov: 33)
• Consequence: POLR1HASP ENST00000688495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

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 (AMR) allele frequency at 95% confidence interval = 0.0599 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-9853A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0527 AC: 8009 AN: 152090 Hom.: 259 Cov.: 33

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0633

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0388

Gnomad SAS AF: 0.0592

Gnomad FIN AF: 0.0238

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.0587

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

GnomAD4 genome AF: 0.0527 AC: 8023 AN: 152208 Hom.: 259 Cov.: 33 AF XY: 0.0531 AC XY: 3955 AN XY: 74434

Gnomad4 AFR AF: 0.0493

Gnomad4 AMR AF: 0.0632

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.0389

Gnomad4 SAS AF: 0.0605

Gnomad4 FIN AF: 0.0238

Gnomad4 NFE AF: 0.0516

Gnomad4 OTH AF: 0.0577

Alfa AF: 0.0571 Hom.: 162

Bravo AF: 0.0538

Asia WGS AF: 0.0450 AC: 156 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	7.6
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3901554; hg19: chr6-29955025;