rs401618

Positions:

• chr6-29982433-A-G
• chr6-29982433-A-T

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-5038T>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 0.234 in 151,518 control chromosomes in the GnomAD database, including 4,554 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 0.23 (4554 hom., cov: 32)
• Consequence: POLR1HASP ENST00000688495.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000688495.1	n.361-5038T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35370 AN: 151408 Hom.: 4544 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35389 AN: 151518 Hom.: 4554 Cov.: 32 AF XY: 0.237 AC XY: 17546 AN XY: 74000

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.291

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.223

Alfa AF: 0.264 Hom.: 3629

Bravo AF: 0.219

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs401618; hg19: chr6-29950210;