chr2-127401685-G-A

Variant names:

• chr2-127401685-G-A
• rs7580658
• ENST00000688447.2:n.316-4130G>A

Variant summary

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

The ENST00000688447.2(MAP3K2-DT):​n.316-4130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,110 control chromosomes in the GnomAD database, including 10,141 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 0.35 (10141 hom., cov: 33)
• Consequence: MAP3K2-DT ENST00000688447.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 17 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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
MAP3K2-DT	ENST00000688447.2	n.316-4130G>A		intron_variant	Intron 3 of 3
MAP3K2-DT	ENST00000778703.1	n.289-4204G>A		intron_variant	Intron 3 of 3
MAP3K2-DT	ENST00000778704.1	n.498-4130G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53178 AN: 151992 Hom.: 10131 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.350 AC: 53215 AN: 152110 Hom.: 10141 Cov.: 33 AF XY: 0.356 AC XY: 26457 AN XY: 74338

African (AFR) AF: 0.222 AC: 9215 AN: 41500

American (AMR) AF: 0.516 AC: 7881 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.621 AC: 3214 AN: 5176

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4820

European-Finnish (FIN) AF: 0.403 AC: 4256 AN: 10572

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.367 AC: 24960 AN: 67964

Other (OTH) AF: 0.353 AC: 748 AN: 2116

Alfa AF: 0.369 Hom.: 19061

Bravo AF: 0.360

Asia WGS AF: 0.432 AC: 1497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7580658; hg19: chr2-128159261;