chr6-29997567-A-G

Variant names:

• chr6-29997567-A-G
• rs6911279
• ENST00000422224.6:n.823-9340T>C

Variant summary

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

The ENST00000422224.6(POLR1HASP):​n.823-9340T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,010 control chromosomes in the GnomAD database, including 2,722 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 0.17 (2722 hom., cov: 32)
• Consequence: POLR1HASP ENST00000422224.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 15 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422224.6. 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	ENST00000422224.6	TSL:3	n.823-9340T>C		intron	N/A
	POLR1HASP	ENST00000688495.1		n.361-20172T>C		intron	N/A
	POLR1HASP	ENST00000849678.1		n.588+24100T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25834 AN: 151892 Hom.: 2704 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.170 AC: 25882 AN: 152010 Hom.: 2722 Cov.: 32 AF XY: 0.168 AC XY: 12522 AN XY: 74318

African (AFR) AF: 0.274 AC: 11366 AN: 41422

American (AMR) AF: 0.210 AC: 3201 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3468

East Asian (EAS) AF: 0.185 AC: 954 AN: 5152

South Asian (SAS) AF: 0.182 AC: 878 AN: 4816

European-Finnish (FIN) AF: 0.0478 AC: 506 AN: 10596

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7443 AN: 67968

Other (OTH) AF: 0.189 AC: 399 AN: 2112

Alfa AF: 0.154 Hom.: 2018

Bravo AF: 0.190

Asia WGS AF: 0.180 AC: 627 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	2.5
DANN	Benign	0.20
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs6911279; hg19: chr6-29965344;