2-127396708-C-G

Variant names:

• chr2-127396708-C-G
• rs6761391
• ENST00000433673.3:n.325-1239C>G

Variant summary

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

The ENST00000433673.3(MAP3K2-DT):​n.325-1239C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,368 control chromosomes in the GnomAD database, including 22,594 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 0.54 (22594 hom., cov: 30)
• Consequence: MAP3K2-DT ENST00000433673.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 3 publications found

Genes affected

MAP3K2-DT (HGNC:54088): (MAP3K2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000433673.3. 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
	MAP3K2-DT	NR_187125.1		n.362-1239C>G		intron	N/A
	MAP3K2-DT	NR_187127.1		n.289-1239C>G		intron	N/A
	MAP3K2-DT	NR_187129.1		n.309-1239C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP3K2-DT	ENST00000433673.3	TSL:1	n.325-1239C>G		intron	N/A
	MAP3K2-DT	ENST00000685004.3		n.287-1239C>G		intron	N/A
	MAP3K2-DT	ENST00000688447.2		n.315+7523C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81644 AN: 151250 Hom.: 22554 Cov.: 30

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.540 AC: 81742 AN: 151368 Hom.: 22594 Cov.: 30 AF XY: 0.541 AC XY: 39985 AN XY: 73880

African (AFR) AF: 0.629 AC: 25971 AN: 41308

American (AMR) AF: 0.626 AC: 9556 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1765 AN: 3462

East Asian (EAS) AF: 0.730 AC: 3763 AN: 5156

South Asian (SAS) AF: 0.366 AC: 1753 AN: 4786

European-Finnish (FIN) AF: 0.476 AC: 4921 AN: 10334

Middle Eastern (MID) AF: 0.503 AC: 147 AN: 292

European-Non Finnish (NFE) AF: 0.476 AC: 32278 AN: 67766

Other (OTH) AF: 0.517 AC: 1087 AN: 2102

Alfa AF: 0.377 Hom.: 957

Bravo AF: 0.560

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.29
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6761391; hg19: chr2-128154284;