6-29964553-T-C

Variant names:

• chr6-29964553-T-C
• rs2517681
• ENST00000849678.1:n.589-17637A>G

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-17637A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,744 control chromosomes in the GnomAD database, including 22,890 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 0.54 (22890 hom., cov: 31)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 12 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=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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.589-17637A>G		intron_variant	Intron 3 of 4
POLR1HASP	ENST00000849679.1	n.65+12050A>G		intron_variant	Intron 1 of 5
POLR1HASP	ENST00000849680.1	n.506-7803A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82578 AN: 151632 Hom.: 22852 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.545 AC: 82651 AN: 151744 Hom.: 22890 Cov.: 31 AF XY: 0.546 AC XY: 40501 AN XY: 74186

African (AFR) AF: 0.565 AC: 23314 AN: 41248

American (AMR) AF: 0.574 AC: 8767 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1618 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3614 AN: 5162

South Asian (SAS) AF: 0.579 AC: 2789 AN: 4820

European-Finnish (FIN) AF: 0.542 AC: 5718 AN: 10552

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35088 AN: 67914

Other (OTH) AF: 0.537 AC: 1129 AN: 2102

Alfa AF: 0.479 Hom.: 5851

Bravo AF: 0.552

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.93
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2517681; hg19: chr6-29932330;