6-29987422-G-T

Variant names:

• chr6-29987422-G-T
• rs5025708
• ENST00000688495.1:n.361-10027C>A

Variant summary

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

The ENST00000688495.1(POLR1HASP):​n.361-10027C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,256 control chromosomes in the GnomAD database, including 64,474 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 0.92 (64474 hom., cov: 32)
• Consequence: POLR1HASP ENST00000688495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 24 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000688495.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000688495.1		n.361-10027C>A		intron	N/A
	POLR1HASP	ENST00000849678.1		n.588+34245C>A		intron	N/A
	POLR1HASP	ENST00000849680.1		n.506-30672C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139792 AN: 152138 Hom.: 64406 Cov.: 32

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.899

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.919 AC: 139919 AN: 152256 Hom.: 64474 Cov.: 32 AF XY: 0.920 AC XY: 68456 AN XY: 74432

African (AFR) AF: 0.974 AC: 40457 AN: 41554

American (AMR) AF: 0.931 AC: 14237 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.919 AC: 3189 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5112 AN: 5182

South Asian (SAS) AF: 0.945 AC: 4567 AN: 4832

European-Finnish (FIN) AF: 0.899 AC: 9517 AN: 10588

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59768 AN: 68020

Other (OTH) AF: 0.918 AC: 1933 AN: 2106

Alfa AF: 0.896 Hom.: 222560

Bravo AF: 0.925

Asia WGS AF: 0.965 AC: 3357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.56
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs5025708; hg19: chr6-29955199;