15-67788548-A-T

Variant names:

• chr15-67788548-A-T
• rs4776970
• NM_145160.3:c.1242+15796A>T

Variant summary

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

The NM_145160.3(MAP2K5):​c.1242+15796A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,150 control chromosomes in the GnomAD database, including 16,149 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 0.45 (16149 hom., cov: 33)
• Consequence: MAP2K5 NM_145160.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693
• Publications: 51 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAP2K5	NM_145160.3	c.1242+15796A>T		intron_variant	Intron 21 of 21	ENST00000178640.10	NP_660143.1
MAP2K5	NM_002757.4	c.1212+15796A>T		intron_variant	Intron 20 of 20		NP_002748.1
MAP2K5	NM_001206804.2	c.1134+15796A>T		intron_variant	Intron 21 of 21		NP_001193733.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAP2K5	ENST00000178640.10	c.1242+15796A>T		intron_variant	Intron 21 of 21	1	NM_145160.3	ENSP00000178640.5

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67801 AN: 152032 Hom.: 16107 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.542

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.446 AC: 67904 AN: 152150 Hom.: 16149 Cov.: 33 AF XY: 0.450 AC XY: 33495 AN XY: 74390

African (AFR) AF: 0.535 AC: 22194 AN: 41480

American (AMR) AF: 0.543 AC: 8302 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1776 AN: 3466

East Asian (EAS) AF: 0.757 AC: 3921 AN: 5178

South Asian (SAS) AF: 0.490 AC: 2365 AN: 4828

European-Finnish (FIN) AF: 0.352 AC: 3725 AN: 10572

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24305 AN: 68018

Other (OTH) AF: 0.459 AC: 971 AN: 2114

Alfa AF: 0.397 Hom.: 7094

Bravo AF: 0.468

Asia WGS AF: 0.668 AC: 2322 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		-0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4776970; hg19: chr15-68080886;