6-29970119-C-T

Variant names:

• chr6-29970119-C-T
• rs3202637
• ENST00000849678.1:n.589-23203G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000849678.1(POLR1HASP):​n.589-23203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 151,928 control chromosomes in the GnomAD database, including 44,664 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 0.77 (44664 hom., cov: 31)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 15 publications found

Genes affected

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POLR1HASP	ENST00000849678.1	n.589-23203G>A		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+6484G>A		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-13369G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116135 AN: 151814 Hom.: 44621 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.817

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.765 AC: 116230 AN: 151928 Hom.: 44664 Cov.: 31 AF XY: 0.764 AC XY: 56772 AN XY: 74288

African (AFR) AF: 0.784 AC: 32384 AN: 41328

American (AMR) AF: 0.793 AC: 12115 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2217 AN: 3466

East Asian (EAS) AF: 0.699 AC: 3610 AN: 5164

South Asian (SAS) AF: 0.712 AC: 3433 AN: 4820

European-Finnish (FIN) AF: 0.817 AC: 8643 AN: 10578

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51257 AN: 67978

Other (OTH) AF: 0.757 AC: 1595 AN: 2108

Alfa AF: 0.759 Hom.: 79910

Bravo AF: 0.769

Asia WGS AF: 0.743 AC: 2585 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	2.2
DANN	Benign	0.19
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs3202637; hg19: chr6-29937896;