rs9260759

Variant names:

• chr6-29967595-C-T
• rs9260759
• ENST00000849678.1:n.589-20679G>A

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-20679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 151,782 control chromosomes in the GnomAD database, including 1,615 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 0.13 (1615 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 16 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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.589-20679G>A		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+9008G>A		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-10845G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20232 AN: 151666 Hom.: 1612 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.0463

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0711

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.134 AC: 20263 AN: 151782 Hom.: 1615 Cov.: 32 AF XY: 0.133 AC XY: 9859 AN XY: 74206

African (AFR) AF: 0.192 AC: 7912 AN: 41232

American (AMR) AF: 0.178 AC: 2721 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 897 AN: 3466

East Asian (EAS) AF: 0.0465 AC: 240 AN: 5166

South Asian (SAS) AF: 0.126 AC: 610 AN: 4824

European-Finnish (FIN) AF: 0.0711 AC: 752 AN: 10572

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.0995 AC: 6760 AN: 67962

Other (OTH) AF: 0.144 AC: 304 AN: 2106

Alfa AF: 0.117 Hom.: 3468

Bravo AF: 0.143

Asia WGS AF: 0.0930 AC: 323 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.5
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs9260759; hg19: chr6-29935372;