chr6-29950325-T-C

Variant names:

• chr6-29950325-T-C
• rs9260378
• ENST00000849678.1:n.589-3409A>G

Variant summary

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

The ENST00000849678.1(POLR1HASP):​n.589-3409A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0821 in 143,758 control chromosomes in the GnomAD database, including 500 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 0.082 (500 hom., cov: 32)
• Consequence: POLR1HASP ENST00000849678.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 2 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POLR1HASP	ENST00000849678.1		n.589-3409A>G		intron	N/A
	POLR1HASP	ENST00000849679.1		n.66-21779A>G		intron	N/A
	POLR1HASP	ENST00000849682.1		n.751-21779A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 11775 AN: 143652 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.0884

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.0486

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.0777

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0953

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

GnomAD4 genome AF: 0.0821 AC: 11802 AN: 143758 Hom.: 500 Cov.: 32 AF XY: 0.0807 AC XY: 5688 AN XY: 70454

African (AFR) AF: 0.114 AC: 4275 AN: 37552

American (AMR) AF: 0.0883 AC: 1258 AN: 14246

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 265 AN: 3258

East Asian (EAS) AF: 0.0157 AC: 75 AN: 4792

South Asian (SAS) AF: 0.0487 AC: 220 AN: 4522

European-Finnish (FIN) AF: 0.0481 AC: 504 AN: 10468

Middle Eastern (MID) AF: 0.0797 AC: 22 AN: 276

European-Non Finnish (NFE) AF: 0.0746 AC: 4908 AN: 65766

Other (OTH) AF: 0.0950 AC: 187 AN: 1968

Alfa AF: 0.0225 Hom.: 9

Bravo AF: 0.0834

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.17
PhyloP100		-1.9

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9260378;

hg19: chr6-29918102;