chr6-29966104-T-A

Variant names:

• chr6-29966104-T-A
• rs6457110
• ENST00000849678.1:n.589-19188A>T

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-19188A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 150,726 control chromosomes in the GnomAD database, including 12,333 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 0.40 (12333 hom., cov: 28)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 28 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 (AMR) allele frequency at 95% confidence interval = 0.428 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.589-19188A>T		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+10499A>T		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-9354A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60341 AN: 150618 Hom.: 12324 Cov.: 28

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.401 AC: 60371 AN: 150726 Hom.: 12333 Cov.: 28 AF XY: 0.400 AC XY: 29395 AN XY: 73556

African (AFR) AF: 0.403 AC: 16421 AN: 40784

American (AMR) AF: 0.436 AC: 6637 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3464

East Asian (EAS) AF: 0.359 AC: 1837 AN: 5112

South Asian (SAS) AF: 0.290 AC: 1390 AN: 4792

European-Finnish (FIN) AF: 0.434 AC: 4459 AN: 10282

Middle Eastern (MID) AF: 0.376 AC: 109 AN: 290

European-Non Finnish (NFE) AF: 0.396 AC: 26873 AN: 67806

Other (OTH) AF: 0.384 AC: 800 AN: 2082

Alfa AF: 0.397 Hom.: 6847

Bravo AF: 0.403

Asia WGS AF: 0.297 AC: 1025 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.3
DANN	Benign	0.65
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs6457110; hg19: chr6-29933881;