rs7739434

Variant names:

• chr6-29962842-G-A
• rs7739434
• ENST00000849678.1:n.589-15926C>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-15926C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 151,854 control chromosomes in the GnomAD database, including 46,616 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 0.78 (46616 hom., cov: 31)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905
• Publications: 17 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.843 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.589-15926C>T		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+13761C>T		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-6092C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118165 AN: 151738 Hom.: 46590 Cov.: 31

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.813

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.779 AC: 118226 AN: 151854 Hom.: 46616 Cov.: 31 AF XY: 0.782 AC XY: 58044 AN XY: 74222

African (AFR) AF: 0.669 AC: 27600 AN: 41236

American (AMR) AF: 0.790 AC: 12056 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.813 AC: 2819 AN: 3466

East Asian (EAS) AF: 0.864 AC: 4466 AN: 5166

South Asian (SAS) AF: 0.796 AC: 3840 AN: 4822

European-Finnish (FIN) AF: 0.863 AC: 9142 AN: 10592

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55620 AN: 67988

Other (OTH) AF: 0.764 AC: 1610 AN: 2108

Alfa AF: 0.809 Hom.: 79109

Bravo AF: 0.768

Asia WGS AF: 0.824 AC: 2846 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs7739434; hg19: chr6-29930619;