rs7580658

Positions:

• chr2-127401685-G-A
• chr2-127401685-G-T

Variant summary

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

The ENST00000688447.1(MAP3K2-DT):​n.304-4130G>A 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 0.35 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 ENST00000688447.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP3K2-DT	ENST00000688447.1	n.304-4130G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.353

Alfa AF: 0.355 Hom.: 4656

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7580658; hg19: chr2-128159261;