rs2734925

Variant names:

• chr6-29913570-G-C
• rs2734925
• ENST00000849679.1:n.493+13814C>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+13814C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 144,372 control chromosomes in the GnomAD database, including 35,994 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 0.68 (35994 hom., cov: 29)
• Consequence: POLR1HASP ENST00000849679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 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+13814C>G		intron_variant	Intron 4 of 5
POLR1HASP	ENST00000849682.1	n.1075-12619C>G		intron_variant	Intron 3 of 3
POLR1HASP	ENST00000849693.1	n.1100-23585C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.685 AC: 98801 AN: 144272 Hom.: 35987 Cov.: 29

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.723

Gnomad AMR AF: 0.677

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.641

Gnomad NFE AF: 0.701

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.685 AC: 98841 AN: 144372 Hom.: 35994 Cov.: 29 AF XY: 0.682 AC XY: 48004 AN XY: 70370

African (AFR) AF: 0.669 AC: 25666 AN: 38344

American (AMR) AF: 0.677 AC: 9559 AN: 14124

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2380 AN: 3348

East Asian (EAS) AF: 0.787 AC: 3663 AN: 4656

South Asian (SAS) AF: 0.690 AC: 3052 AN: 4426

European-Finnish (FIN) AF: 0.590 AC: 5992 AN: 10158

Middle Eastern (MID) AF: 0.629 AC: 175 AN: 278

European-Non Finnish (NFE) AF: 0.701 AC: 46424 AN: 66208

Other (OTH) AF: 0.663 AC: 1292 AN: 1948

Alfa AF: 0.696 Hom.: 4217

Asia WGS AF: 0.685 AC: 2138 AN: 3118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2734925; hg19: chr6-29881347;