rs7753357

chr6-136679420-T-A

Variant summary

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

The NM_005923.4(MAP3K5):c.1254-10025A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,136 control chromosomes in the GnomAD database, including 4,029 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 0.18 (4029 hom., cov: 32)
• Consequence: MAP3K5 NM_005923.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

MAP3K5 (HGNC:6857): (mitogen-activated protein kinase kinase kinase 5) Mitogen-activated protein kinase (MAPK) signaling cascades include MAPK or extracellular signal-regulated kinase (ERK), MAPK kinase (MKK or MEK), and MAPK kinase kinase (MAPKKK or MEKK). MAPKK kinase/MEKK phosphorylates and activates its downstream protein kinase, MAPK kinase/MEK, which in turn activates MAPK. The kinases of these signaling cascades are highly conserved, and homologs exist in yeast, Drosophila, and mammalian cells. MAPKKK5 contains 1,374 amino acids with all 11 kinase subdomains. Northern blot analysis shows that MAPKKK5 transcript is abundantly expressed in human heart and pancreas. The MAPKKK5 protein phosphorylates and activates MKK4 (aliases SERK1, MAPKK4) in vitro, and activates c-Jun N-terminal kinase (JNK)/stress-activated protein kinase (SAPK) during transient expression in COS and 293 cells; MAPKKK5 does not activate MAPK/ERK. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP3K5	NM_005923.4	c.1254-10025A>T		intron_variant		ENST00000359015.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP3K5	ENST00000359015.5	c.1254-10025A>T		intron_variant		1	NM_005923.4	P1
MAP3K5	ENST00000698928.1	c.1581-10025A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27609 AN: 152018 Hom.: 4000 Cov.: 32

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.0948

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.182 AC: 27691 AN: 152136 Hom.: 4029 Cov.: 32 AF XY: 0.179 AC XY: 13336 AN XY: 74364

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0943

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0865

Gnomad4 OTH AF: 0.208

Alfa AF: 0.141 Hom.: 306

Bravo AF: 0.203

Asia WGS AF: 0.183 AC: 634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753357; hg19: chr6-137000558;