15-67767841-G-A

Position:

• chr15-67767841-G-A

Variant summary

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

The NM_145160.3(MAP2K5):​c.1135-1761G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 151,874 control chromosomes in the GnomAD database, including 9,767 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 0.36 (9767 hom., cov: 31)
• Consequence: MAP2K5 NM_145160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.37

Genes affected

MAP2K5 (HGNC:6845): (mitogen-activated protein kinase kinase 5) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase specifically interacts with and activates MAPK7/ERK5. This kinase itself can be phosphorylated and activated by MAP3K3/MEKK3, as well as by atypical protein kinase C isoforms (aPKCs). The signal cascade mediated by this kinase is involved in growth factor stimulated cell proliferation and muscle cell differentiation. Three alternatively spliced transcript variants of this gene encoding distinct isoforms have been described. [provided by RefSeq, May 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP2K5	NM_145160.3	c.1135-1761G>A		intron_variant		ENST00000178640.10	NP_660143.1
MAP2K5	NM_001206804.2	c.1027-1761G>A		intron_variant			NP_001193733.1
MAP2K5	NM_002757.4	c.1105-1761G>A		intron_variant			NP_002748.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP2K5	ENST00000178640.10	c.1135-1761G>A		intron_variant		1	NM_145160.3	ENSP00000178640	P1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54061 AN: 151756 Hom.: 9754 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.356 AC: 54096 AN: 151874 Hom.: 9767 Cov.: 31 AF XY: 0.363 AC XY: 26970 AN XY: 74208

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.337

Alfa AF: 0.338 Hom.: 9621

Bravo AF: 0.340

Asia WGS AF: 0.396 AC: 1374 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.025
DANN	Benign	0.63

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: rs745212; hg19: chr15-68060179;