6-106074152-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651185.1(PRDM1):c.-66-14049T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 152,262 control chromosomes in the GnomAD database, including 56,349 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 0.86 (56349 hom., cov: 32)
• Consequence: PRDM1 ENST00000651185.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

ATG5 (HGNC:589): (autophagy related 5) The protein encoded by this gene, in combination with autophagy protein 12, functions as an E1-like activating enzyme in a ubiquitin-like conjugating system. The encoded protein is involved in several cellular processes, including autophagic vesicle formation, mitochondrial quality control after oxidative damage, negative regulation of the innate antiviral immune response, lymphocyte development and proliferation, MHC II antigen presentation, adipocyte differentiation, and apoptosis. Several transcript variants encoding different protein isoforms have been found for this gene. [provided by RefSeq, Sep 2015]

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRDM1	XM_017011187.2	c.-66-14049T>C		intron_variant
PRDM1	XM_047419246.1	c.-66-14049T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ATG5	ENST00000636437.1	c.458-27327A>G		intron_variant		5
PRDM1	ENST00000651185.1	c.-66-14049T>C		intron_variant				P4
PRDM1	ENST00000652320.1	c.-66-14049T>C		intron_variant				P4
ATG5	ENST00000636335.1	c.*39-1941A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.856 AC: 130300 AN: 152144 Hom.: 56281 Cov.: 32

Gnomad AFR AF: 0.964

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.936

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.836

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

GnomAD4 genome AF: 0.857 AC: 130427 AN: 152262 Hom.: 56349 Cov.: 32 AF XY: 0.858 AC XY: 63889 AN XY: 74436

Gnomad4 AFR AF: 0.965

Gnomad4 AMR AF: 0.861

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.935

Gnomad4 FIN AF: 0.774

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.838

Alfa AF: 0.802 Hom.: 54764

Bravo AF: 0.865

Asia WGS AF: 0.957 AC: 3326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.8
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6911490; hg19: chr6-106522027;