chr6-29970248-G-A

Variant names:

• chr6-29970248-G-A
• rs6457116
• ENST00000849678.1:n.589-23332C>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-23332C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0515 in 152,222 control chromosomes in the GnomAD database, including 277 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 0.051 (277 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 8 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 (AMR) allele frequency at 95% confidence interval = 0.0822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849678.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849678.1		n.589-23332C>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+6355C>T		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-13498C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0515 AC: 7827 AN: 152104 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0846

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0860

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0303

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0515 AC: 7838 AN: 152222 Hom.: 277 Cov.: 32 AF XY: 0.0514 AC XY: 3826 AN XY: 74422

African (AFR) AF: 0.0845 AC: 3511 AN: 41530

American (AMR) AF: 0.0860 AC: 1315 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3472

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5182

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4816

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10608

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0303 AC: 2063 AN: 68002

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0375 Hom.: 115

Bravo AF: 0.0563

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.90
DANN	Benign	0.17
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs6457116; hg19: chr6-29938025;