ENST00000549066.1:c.109-31803T>A

Variant names:

• chr12-101882429-T-A
• NM_018370.3:c.131+4509T>A

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018370.3(DRAM1):​c.131+4509T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: DRAM1 NM_018370.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.422

Genes affected

DRAM1 (HGNC:25645): (DNA damage regulated autophagy modulator 1) This gene is regulated as part of the p53 tumor suppressor pathway. The gene encodes a lysosomal membrane protein that is required for the induction of autophagy by the pathway. Decreased transcriptional expression of this gene is associated with various tumors. This gene has a pseudogene on chromosome 4. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DRAM1	NM_018370.3	c.131+4509T>A		intron_variant	Intron 1 of 6	ENST00000258534.13	NP_060840.2
DRAM1	XM_005269004.3	c.131+4509T>A		intron_variant	Intron 1 of 5		XP_005269061.1
DRAM1	XM_005269005.3	c.131+4509T>A		intron_variant	Intron 1 of 4		XP_005269062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAM1	ENST00000258534.13	c.131+4509T>A		intron_variant	Intron 1 of 6	1	NM_018370.3	ENSP00000258534.8
DRAM1	ENST00000549365.1	n.122+4509T>A		intron_variant	Intron 1 of 4	3		ENSP00000447171.1
DRAM1	ENST00000544152.5	c.131+4509T>A		intron_variant	Intron 1 of 3	2		ENSP00000445827.1
DRAM1	ENST00000551403.1	n.131+4509T>A		intron_variant	Intron 1 of 5	5		ENSP00000448075.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	5.9
DANN	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-102276207;