rs6911690

Variant names:

• chr6-106023088-G-A
• rs6911690
• ENST00000652320.1:c.-67+29449G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-106023088-G-A
• chr6-106023088-G-C

Variant summary

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

The ENST00000652320.1(PRDM1):​c.-67+29449G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,198 control chromosomes in the GnomAD database, including 63,055 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 0.91 (63055 hom., cov: 31)
• Consequence: PRDM1 ENST00000652320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 10 publications found

Genes affected

PRDM1 (HGNC:9346): (PR/SET domain 1) This gene encodes a protein that acts as a repressor of beta-interferon gene expression. The protein binds specifically to the PRDI (positive regulatory domain I element) of the beta-IFN gene promoter. Transcription of this gene increases upon virus induction. Two alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652320.1. 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
	PRDM1	ENST00000652320.1		c.-67+29449G>A		intron	N/A	ENSP00000498580.1	O75626-2

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138276 AN: 152080 Hom.: 62997 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.936

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.863

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.909 AC: 138393 AN: 152198 Hom.: 63055 Cov.: 31 AF XY: 0.911 AC XY: 67790 AN XY: 74414

African (AFR) AF: 0.955 AC: 39662 AN: 41528

American (AMR) AF: 0.890 AC: 13595 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2867 AN: 3472

East Asian (EAS) AF: 0.834 AC: 4304 AN: 5160

South Asian (SAS) AF: 0.942 AC: 4544 AN: 4824

European-Finnish (FIN) AF: 0.918 AC: 9733 AN: 10598

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60713 AN: 68016

Other (OTH) AF: 0.883 AC: 1866 AN: 2114

Alfa AF: 0.904 Hom.: 3283

Bravo AF: 0.906

Asia WGS AF: 0.913 AC: 3174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.69
PhyloP100		-0.66

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: rs6911690;

hg19: chr6-106470963;