12-123600955-G-A

Variant names:

• chr12-123600955-G-A
• rs786425
• ENST00000793071.1:n.360+721C>T

Variant summary

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

The ENST00000793071.1(TMED2-DT):​n.360+721C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.462 in 152,090 control chromosomes in the GnomAD database, including 20,188 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 0.46 (20188 hom., cov: 31)
• Consequence: TMED2-DT ENST00000793071.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 17 publications found

Genes affected

TMED2-DT (HGNC:53346): (TMED2 divergent transcript)

ENSG00000303254 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793071.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMED2-DT	ENST00000793071.1		n.360+721C>T		intron	N/A
	TMED2-DT	ENST00000793072.1		n.360+721C>T		intron	N/A
	TMED2-DT	ENST00000793073.1		n.314+752C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70315 AN: 151974 Hom.: 20185 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.697

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.462 AC: 70325 AN: 152090 Hom.: 20188 Cov.: 31 AF XY: 0.472 AC XY: 35119 AN XY: 74334

African (AFR) AF: 0.115 AC: 4795 AN: 41522

American (AMR) AF: 0.595 AC: 9077 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2001 AN: 3468

East Asian (EAS) AF: 0.868 AC: 4482 AN: 5162

South Asian (SAS) AF: 0.554 AC: 2668 AN: 4816

European-Finnish (FIN) AF: 0.697 AC: 7373 AN: 10582

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38323 AN: 67970

Other (OTH) AF: 0.501 AC: 1058 AN: 2112

Alfa AF: 0.386 Hom.: 5807

Bravo AF: 0.445

Asia WGS AF: 0.664 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	9.5
DANN	Benign	0.81
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs786425; hg19: chr12-124085502;