rs12190966

chr6-145825684-T-G

Variant summary

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

The NR_038246.1(EPM2A-DT):n.53-2677T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.453 in 151,952 control chromosomes in the GnomAD database, including 16,210 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 0.45 (16210 hom., cov: 32)
• Consequence: EPM2A-DT NR_038246.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

Genes affected

EPM2A-DT (HGNC:48990): (EPM2A divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EPM2A-DT	NR_038246.1	n.53-2677T>G		intron_variant, non_coding_transcript_variant
EPM2A-DT	NR_038244.1	n.557-2677T>G		intron_variant, non_coding_transcript_variant
EPM2A-DT	NR_038245.1	n.557-2677T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EPM2A-DT	ENST00000629681.1	n.207+15790T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68830 AN: 151832 Hom.: 16185 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.508

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.453 AC: 68902 AN: 151952 Hom.: 16210 Cov.: 32 AF XY: 0.456 AC XY: 33834 AN XY: 74264

Gnomad4 AFR AF: 0.561

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.508

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.441

Alfa AF: 0.427 Hom.: 1774

Bravo AF: 0.445

Asia WGS AF: 0.457 AC: 1589 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.14
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12190966; hg19: chr6-146146820;