rs10507137

Variant names:

• chr12-101963532-A-G
• rs10507137
• ENST00000549066.1:c.109-48281A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-101963532-A-G
• chr12-101963532-A-T

Variant summary

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

The ENST00000549066.1(DRAM1):​c.109-48281A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,978 control chromosomes in the GnomAD database, including 17,008 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 0.47 (17008 hom., cov: 31)
• Consequence: DRAM1 ENST00000549066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.684
• Publications: 2 publications found

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]

DRAM1-AS1 (HGNC:53335):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549066.1. 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
	DRAM1	ENST00000549066.1	TSL:3	c.109-48281A>G		intron	N/A	ENSP00000447906.1	H0YHV0
	DRAM1-AS1	ENST00000845155.1		n.461+620T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70672 AN: 151860 Hom.: 17001 Cov.: 31

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.465 AC: 70705 AN: 151978 Hom.: 17008 Cov.: 31 AF XY: 0.456 AC XY: 33875 AN XY: 74294

African (AFR) AF: 0.536 AC: 22226 AN: 41428

American (AMR) AF: 0.471 AC: 7197 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1386 AN: 3470

East Asian (EAS) AF: 0.106 AC: 549 AN: 5170

South Asian (SAS) AF: 0.283 AC: 1365 AN: 4822

European-Finnish (FIN) AF: 0.416 AC: 4384 AN: 10540

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32151 AN: 67946

Other (OTH) AF: 0.432 AC: 909 AN: 2102

Alfa AF: 0.464 Hom.: 28515

Bravo AF: 0.474

Asia WGS AF: 0.200 AC: 695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.41
DANN	Benign	0.47
PhyloP100		-0.68

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: rs10507137;

hg19: chr12-102357310;