chr6-29913048-T-C

Variant names:

• chr6-29913048-T-C
• rs1611442
• ENST00000849679.1:n.493+14336A>G

Variant summary

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

The ENST00000849679.1(POLR1HASP):​n.493+14336A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 145,924 control chromosomes in the GnomAD database, including 52,269 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 0.83 (52269 hom., cov: 28)
• Consequence: POLR1HASP ENST00000849679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 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	ENST00000849679.1	n.493+14336A>G		intron_variant	Intron 4 of 5
POLR1HASP	ENST00000849682.1	n.1075-12097A>G		intron_variant	Intron 3 of 3
POLR1HASP	ENST00000849693.1	n.1100-23063A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 120551 AN: 145814 Hom.: 52216 Cov.: 28

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.761

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.859

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.827 AC: 120660 AN: 145924 Hom.: 52269 Cov.: 28 AF XY: 0.823 AC XY: 58422 AN XY: 71020

African (AFR) AF: 0.887 AC: 34860 AN: 39308

American (AMR) AF: 0.867 AC: 12343 AN: 14232

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2922 AN: 3384

East Asian (EAS) AF: 0.977 AC: 4571 AN: 4680

South Asian (SAS) AF: 0.882 AC: 3911 AN: 4436

European-Finnish (FIN) AF: 0.649 AC: 6609 AN: 10182

Middle Eastern (MID) AF: 0.853 AC: 237 AN: 278

European-Non Finnish (NFE) AF: 0.794 AC: 52838 AN: 66536

Other (OTH) AF: 0.847 AC: 1693 AN: 2000

Alfa AF: 0.816 Hom.: 5681

Asia WGS AF: 0.928 AC: 2888 AN: 3112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.12
DANN	Benign	0.64
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1611442; hg19: chr6-29880825;