rs9332443

Variant names:

• chr12-101977525-G-A
• rs9332443
• ENST00000549066.1:c.109-34288G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-101977525-G-A
• chr12-101977525-G-T

Variant summary

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

The ENST00000549066.1(DRAM1):​c.109-34288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,984 control chromosomes in the GnomAD database, including 3,970 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 0.20 (3970 hom., cov: 32)
• Consequence: DRAM1 ENST00000549066.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.413

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DRAM1	ENST00000549066.1	c.109-34288G>A		intron_variant	Intron 2 of 2	3		ENSP00000447906.1

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30146 AN: 151866 Hom.: 3948 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.118

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.199 AC: 30215 AN: 151984 Hom.: 3970 Cov.: 32 AF XY: 0.212 AC XY: 15731 AN XY: 74276

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.118

Gnomad4 OTH AF: 0.207

Alfa AF: 0.137 Hom.: 2451

Bravo AF: 0.197

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.8
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332443; hg19: chr12-102371303;